diff --git a/packages/react-native/ReactCommon/react/renderer/viewtransition/ViewTransitionModule.cpp b/packages/react-native/ReactCommon/react/renderer/viewtransition/ViewTransitionModule.cpp
index 39983aaa7895..672802ed7aa6 100644
--- a/packages/react-native/ReactCommon/react/renderer/viewtransition/ViewTransitionModule.cpp
+++ b/packages/react-native/ReactCommon/react/renderer/viewtransition/ViewTransitionModule.cpp
@@ -7,6 +7,7 @@
 
 #include "ViewTransitionModule.h"
 
+#include <cxxreact/TraceSection.h>
 #include <glog/logging.h>
 #include <react/renderer/components/root/RootShadowNode.h>
 #include <react/renderer/core/LayoutableShadowNode.h>
@@ -72,6 +73,7 @@ void ViewTransitionModule::applyViewTransitionName(
     const ShadowNode& shadowNode,
     const std::string& name,
     const std::string& /*className*/) {
+  TraceSection s("ViewTransitionModule::applyViewTransitionName", "name", name);
   auto tag = shadowNode.getTag();
   auto surfaceId = shadowNode.getSurfaceId();
 
@@ -86,14 +88,22 @@ void ViewTransitionModule::applyViewTransitionName(
       .size = layoutMetrics.frame.size,
       .pointScaleFactor = layoutMetrics.pointScaleFactor};
 
-  nameRegistry_[tag].insert(name);
-
-  // If applyViewTransitionName is called after transition started, this is the
-  // "new" state (end snapshot). Otherwise, this is the "old" state (start
-  // snapshot)
-  if (!transitionStarted_) {
+  // Calls outside mutationCallback are from the before-mutation phase (old
+  // state for an upcoming transition). Assign a provisional next transition ID
+  // so startViewTransitionEnd cleanup preserves these entries.
+  auto currentTransitionId =
+      insideMutationCallback_ ? activeTransitionId_ : activeTransitionId_ + 1;
+  nameRegistry_[tag].names.insert(name);
+  nameRegistry_[tag].transitionId = currentTransitionId;
+
+  // Old state: called outside mutationCallback (before-mutation phase).
+  // New state: called inside mutationCallback (after-mutation phase).
+  if (!insideMutationCallback_) {
     AnimationKeyFrameView oldView{
-        .layoutMetrics = keyframeMetrics, .tag = tag, .surfaceId = surfaceId};
+        .layoutMetrics = keyframeMetrics,
+        .tag = tag,
+        .surfaceId = surfaceId,
+        .transitionId = currentTransitionId};
     oldLayout_[name] = oldView;
 
     // Request the platform to capture a bitmap snapshot of the old view
@@ -101,6 +111,10 @@ void ViewTransitionModule::applyViewTransitionName(
     if (uiManager_ != nullptr) {
       auto* delegate = uiManager_->getDelegate();
       if (delegate != nullptr) {
+        TraceSection snapshotSection(
+            "ViewTransitionModule::applyViewTransitionName - uiManagerDidCaptureViewSnapshot",
+            "name",
+            name);
         delegate->uiManagerDidCaptureViewSnapshot(tag, surfaceId);
       }
     }
@@ -111,6 +125,11 @@ void ViewTransitionModule::applyViewTransitionName(
       auto& pseudoElementsBySourceTag = it->second;
       auto innerIt = pseudoElementsBySourceTag.find(tag);
 
+      TraceSection clonePseudoElementSection(
+          "ViewTransitionModule::applyViewTransitionName - maybeClonePseudoElement",
+          "name",
+          name);
+
       if (innerIt != pseudoElementsBySourceTag.end()) {
         // Only clone the pseudo-element if the layout metrics changed
         // since it was last created/refreshed (e.g. due to scrolling or
@@ -147,7 +166,10 @@ void ViewTransitionModule::applyViewTransitionName(
 
   } else {
     AnimationKeyFrameView newView{
-        .layoutMetrics = keyframeMetrics, .tag = tag, .surfaceId = surfaceId};
+        .layoutMetrics = keyframeMetrics,
+        .tag = tag,
+        .surfaceId = surfaceId,
+        .transitionId = activeTransitionId_};
     newLayout_[name] = newView;
   }
 }
@@ -155,6 +177,8 @@ void ViewTransitionModule::applyViewTransitionName(
 void ViewTransitionModule::createViewTransitionInstance(
     const std::string& name,
     Tag pseudoElementTag) {
+  TraceSection s(
+      "ViewTransitionModule::createViewTransitionInstance", "name", name);
   if (uiManager_ == nullptr) {
     return;
   }
@@ -209,6 +233,7 @@ RootShadowNode::Unshared ViewTransitionModule::shadowTreeWillCommit(
   if (oldPseudoElementNodes_.empty()) {
     return newRootShadowNode;
   }
+  TraceSection s("ViewTransitionModule::shadowTreeWillCommit");
 
   auto surfaceId = shadowTree.getSurfaceId();
 
@@ -316,12 +341,14 @@ void ViewTransitionModule::cancelViewTransitionName(
 
 void ViewTransitionModule::restoreViewTransitionName(
     const ShadowNode& shadowNode) {
-  nameRegistry_[shadowNode.getTag()].merge(
+  nameRegistry_[shadowNode.getTag()].names.merge(
       cancelledNameRegistry_[shadowNode.getTag()]);
   cancelledNameRegistry_.erase(shadowNode.getTag());
 }
 
 void ViewTransitionModule::applySnapshotsOnPseudoElementShadowNodes() {
+  TraceSection s(
+      "ViewTransitionModule::applySnapshotsOnPseudoElementShadowNodes");
   if (oldPseudoElementNodes_.empty() || uiManager_ == nullptr) {
     return;
   }
@@ -342,6 +369,7 @@ void ViewTransitionModule::applySnapshotsOnPseudoElementShadowNodes() {
 
 LayoutMetrics ViewTransitionModule::captureLayoutMetricsFromRoot(
     const ShadowNode& shadowNode) {
+  TraceSection s("ViewTransitionModule::captureLayoutMetricsFromRoot");
   if (uiManager_ == nullptr) {
     return EmptyLayoutMetrics;
   }
@@ -387,13 +415,22 @@ void ViewTransitionModule::startViewTransition(
 
   // Mark transition as started
   transitionStarted_ = true;
+  activeTransitionId_ = ++transitionIdCounter_;
+
+  TraceSection s(
+      "ViewTransitionModule::startViewTransition",
+      "transitionId",
+      activeTransitionId_);
+
   pendingAnimationIds_.clear();
   onCompleteCallback_ = onCompleteCallback;
 
   // Call mutation callback (including commitRoot, measureInstance,
   // applyViewTransitionName, createViewTransitionInstance for old & new)
   if (mutationCallback) {
+    insideMutationCallback_ = true;
     mutationCallback();
+    insideMutationCallback_ = false;
   }
 
   applySnapshotsOnPseudoElementShadowNodes();
@@ -442,13 +479,32 @@ void ViewTransitionModule::suspendOnActiveViewTransition() {
 }
 
 void ViewTransitionModule::startViewTransitionEnd() {
-  for (const auto& [tag, names] : nameRegistry_) {
-    for (const auto& name : names) {
-      oldLayout_.erase(name);
-      newLayout_.erase(name);
+  TraceSection s(
+      "ViewTransitionModule::startViewTransitionEnd",
+      "transitionId",
+      activeTransitionId_);
+  auto finishedId = activeTransitionId_;
+
+  // Only clear layout and registry entries belonging to the finished
+  // transition. A suspended transition's before-mutation phase may have
+  // already written entries with a newer transitionId — preserve those.
+  for (auto it = nameRegistry_.begin(); it != nameRegistry_.end();) {
+    if (it->second.transitionId == finishedId) {
+      for (const auto& name : it->second.names) {
+        if (auto oit = oldLayout_.find(name);
+            oit != oldLayout_.end() && oit->second.transitionId == finishedId) {
+          oldLayout_.erase(oit);
+        }
+        if (auto nit = newLayout_.find(name);
+            nit != newLayout_.end() && nit->second.transitionId == finishedId) {
+          newLayout_.erase(nit);
+        }
+      }
+      it = nameRegistry_.erase(it);
+    } else {
+      ++it;
     }
   }
-  nameRegistry_.clear();
   oldPseudoElementNodes_.clear();
 
   // Clear any pending bitmap snapshots that were captured but never consumed.
diff --git a/packages/react-native/ReactCommon/react/renderer/viewtransition/ViewTransitionModule.h b/packages/react-native/ReactCommon/react/renderer/viewtransition/ViewTransitionModule.h
index 28f7f2f86113..ea3583794881 100644
--- a/packages/react-native/ReactCommon/react/renderer/viewtransition/ViewTransitionModule.h
+++ b/packages/react-native/ReactCommon/react/renderer/viewtransition/ViewTransitionModule.h
@@ -98,17 +98,25 @@ class ViewTransitionModule : public UIManagerViewTransitionDelegate,
     AnimationKeyFrameViewLayoutMetrics layoutMetrics;
     Tag tag{0};
     SurfaceId surfaceId{0};
+    uint32_t transitionId{0};
   };
 
  private:
+  uint32_t transitionIdCounter_{0};
+  uint32_t activeTransitionId_{0};
+
   // registry of layout of old/new views
   std::unordered_map<std::string, AnimationKeyFrameView> oldLayout_{};
   std::unordered_map<std::string, AnimationKeyFrameView> newLayout_{};
-  // tag -> names registry, populated during applyViewTransitionName
+  // tag -> (names, transitionId) registry, populated during applyViewTransitionName
   // Note that tag and name are not 1:1 mapping
   // - In some nested composition 2 names are mappped to the same tag
   // - tags of old and new views are mapped to the same name(s)
-  std::unordered_map<Tag, std::unordered_set<std::string>> nameRegistry_{};
+  struct NameRegistryEntry {
+    std::unordered_set<std::string> names;
+    uint32_t transitionId{0};
+  };
+  std::unordered_map<Tag, NameRegistryEntry> nameRegistry_{};
 
   // used for cancel/restore viewTransitionName
   std::unordered_map<Tag, std::unordered_set<std::string>> cancelledNameRegistry_{};
@@ -138,6 +146,8 @@ class ViewTransitionModule : public UIManagerViewTransitionDelegate,
 
   bool transitionStarted_{false};
 
+  bool insideMutationCallback_{false};
+
   bool transitionReadyFinished_{false};
 
   // When suspendNextTransition_ is true and a transition is active, the next
diff --git a/packages/react-native/scripts/featureflags/ReactNativeFeatureFlags.config.js b/packages/react-native/scripts/featureflags/ReactNativeFeatureFlags.config.js
index 0bf9d70039b6..a07eb630de84 100644
--- a/packages/react-native/scripts/featureflags/ReactNativeFeatureFlags.config.js
+++ b/packages/react-native/scripts/featureflags/ReactNativeFeatureFlags.config.js
@@ -981,6 +981,17 @@ const definitions: FeatureFlagDefinitions = {
 
   jsOnly: {
     ...testDefinitions.jsOnly,
+    animatedDeferStartOfTimingAnimations: {
+      defaultValue: false,
+      metadata: {
+        dateAdded: '2026-05-26',
+        description:
+          'When enabled, native timing animations defer their first frame and re-anchor timing to prevent skipping initial frames when the UI thread is busy with layout work.',
+        expectedReleaseValue: true,
+        purpose: 'experimentation',
+      },
+      ossReleaseStage: 'none',
+    },
     animatedShouldDebounceQueueFlush: {
       defaultValue: false,
       metadata: {
diff --git a/packages/react-native/src/private/featureflags/ReactNativeFeatureFlags.js b/packages/react-native/src/private/featureflags/ReactNativeFeatureFlags.js
index 8b92e20f338b..a55d306356ee 100644
--- a/packages/react-native/src/private/featureflags/ReactNativeFeatureFlags.js
+++ b/packages/react-native/src/private/featureflags/ReactNativeFeatureFlags.js
@@ -4,7 +4,7 @@
  * This source code is licensed under the MIT license found in the
  * LICENSE file in the root directory of this source tree.
  *
- * @generated SignedSource<<7f48f734cd7a098d04cb147980ef364a>>
+ * @generated SignedSource<<a464b9ef1056058917da8b9a70c903a3>>
  * @flow strict
  * @noformat
  */
@@ -29,6 +29,7 @@ import {
 
 export type ReactNativeFeatureFlagsJsOnly = $ReadOnly<{
   jsOnlyTestFlag: Getter<boolean>,
+  animatedDeferStartOfTimingAnimations: Getter<boolean>,
   animatedShouldDebounceQueueFlush: Getter<boolean>,
   animatedShouldUseSingleOp: Getter<boolean>,
   deferFlatListFocusChangeRenderUpdate: Getter<boolean>,
@@ -140,6 +141,11 @@ export type ReactNativeFeatureFlags = $ReadOnly<{
  */
 export const jsOnlyTestFlag: Getter<boolean> = createJavaScriptFlagGetter('jsOnlyTestFlag', false);
 
+/**
+ * When enabled, native timing animations defer their first frame and re-anchor timing to prevent skipping initial frames when the UI thread is busy with layout work.
+ */
+export const animatedDeferStartOfTimingAnimations: Getter<boolean> = createJavaScriptFlagGetter('animatedDeferStartOfTimingAnimations', false);
+
 /**
  * Enables an experimental flush-queue debouncing in Animated.js.
  */
diff --git a/scripts/cxx-api/api-snapshots/ReactAndroidDebugCxx.api b/scripts/cxx-api/api-snapshots/ReactAndroidDebugCxx.api
index 2b4fbb3a4986..5bbaffe84b69 100644
--- a/scripts/cxx-api/api-snapshots/ReactAndroidDebugCxx.api
+++ b/scripts/cxx-api/api-snapshots/ReactAndroidDebugCxx.api
@@ -5453,6 +5453,7 @@ struct facebook::react::ViewTransitionModule::AnimationKeyFrameView {
   public facebook::react::SurfaceId surfaceId;
   public facebook::react::Tag tag;
   public facebook::react::ViewTransitionModule::AnimationKeyFrameViewLayoutMetrics layoutMetrics;
+  public uint32_t transitionId;
 }
 
 struct facebook::react::ViewTransitionModule::AnimationKeyFrameViewLayoutMetrics {
diff --git a/scripts/cxx-api/api-snapshots/ReactAndroidNewarchCxx.api b/scripts/cxx-api/api-snapshots/ReactAndroidNewarchCxx.api
index 06d8694b4b82..f41430b9759f 100644
--- a/scripts/cxx-api/api-snapshots/ReactAndroidNewarchCxx.api
+++ b/scripts/cxx-api/api-snapshots/ReactAndroidNewarchCxx.api
@@ -5279,6 +5279,7 @@ struct facebook::react::ViewTransitionModule::AnimationKeyFrameView {
   public facebook::react::SurfaceId surfaceId;
   public facebook::react::Tag tag;
   public facebook::react::ViewTransitionModule::AnimationKeyFrameViewLayoutMetrics layoutMetrics;
+  public uint32_t transitionId;
 }
 
 struct facebook::react::ViewTransitionModule::AnimationKeyFrameViewLayoutMetrics {
diff --git a/scripts/cxx-api/api-snapshots/ReactAndroidReleaseCxx.api b/scripts/cxx-api/api-snapshots/ReactAndroidReleaseCxx.api
index 1f7567f39773..b70b7f31f3e5 100644
--- a/scripts/cxx-api/api-snapshots/ReactAndroidReleaseCxx.api
+++ b/scripts/cxx-api/api-snapshots/ReactAndroidReleaseCxx.api
@@ -5444,6 +5444,7 @@ struct facebook::react::ViewTransitionModule::AnimationKeyFrameView {
   public facebook::react::SurfaceId surfaceId;
   public facebook::react::Tag tag;
   public facebook::react::ViewTransitionModule::AnimationKeyFrameViewLayoutMetrics layoutMetrics;
+  public uint32_t transitionId;
 }
 
 struct facebook::react::ViewTransitionModule::AnimationKeyFrameViewLayoutMetrics {
diff --git a/scripts/cxx-api/api-snapshots/ReactAppleDebugCxx.api b/scripts/cxx-api/api-snapshots/ReactAppleDebugCxx.api
index d4f7c124a3cb..008787a98b0c 100644
--- a/scripts/cxx-api/api-snapshots/ReactAppleDebugCxx.api
+++ b/scripts/cxx-api/api-snapshots/ReactAppleDebugCxx.api
@@ -8031,6 +8031,7 @@ struct facebook::react::ViewTransitionModule::AnimationKeyFrameView {
   public facebook::react::SurfaceId surfaceId;
   public facebook::react::Tag tag;
   public facebook::react::ViewTransitionModule::AnimationKeyFrameViewLayoutMetrics layoutMetrics;
+  public uint32_t transitionId;
 }
 
 struct facebook::react::ViewTransitionModule::AnimationKeyFrameViewLayoutMetrics {
diff --git a/scripts/cxx-api/api-snapshots/ReactAppleNewarchCxx.api b/scripts/cxx-api/api-snapshots/ReactAppleNewarchCxx.api
index cd89d347ccfa..c0dd7c1584c6 100644
--- a/scripts/cxx-api/api-snapshots/ReactAppleNewarchCxx.api
+++ b/scripts/cxx-api/api-snapshots/ReactAppleNewarchCxx.api
@@ -7506,6 +7506,7 @@ struct facebook::react::ViewTransitionModule::AnimationKeyFrameView {
   public facebook::react::SurfaceId surfaceId;
   public facebook::react::Tag tag;
   public facebook::react::ViewTransitionModule::AnimationKeyFrameViewLayoutMetrics layoutMetrics;
+  public uint32_t transitionId;
 }
 
 struct facebook::react::ViewTransitionModule::AnimationKeyFrameViewLayoutMetrics {
diff --git a/scripts/cxx-api/api-snapshots/ReactAppleReleaseCxx.api b/scripts/cxx-api/api-snapshots/ReactAppleReleaseCxx.api
index 8219222a7c4d..6cc424cc9d43 100644
--- a/scripts/cxx-api/api-snapshots/ReactAppleReleaseCxx.api
+++ b/scripts/cxx-api/api-snapshots/ReactAppleReleaseCxx.api
@@ -8022,6 +8022,7 @@ struct facebook::react::ViewTransitionModule::AnimationKeyFrameView {
   public facebook::react::SurfaceId surfaceId;
   public facebook::react::Tag tag;
   public facebook::react::ViewTransitionModule::AnimationKeyFrameViewLayoutMetrics layoutMetrics;
+  public uint32_t transitionId;
 }
 
 struct facebook::react::ViewTransitionModule::AnimationKeyFrameViewLayoutMetrics {
diff --git a/scripts/cxx-api/api-snapshots/ReactCommonDebugCxx.api b/scripts/cxx-api/api-snapshots/ReactCommonDebugCxx.api
index 5f68b22fb882..2e43b23d2fc1 100644
--- a/scripts/cxx-api/api-snapshots/ReactCommonDebugCxx.api
+++ b/scripts/cxx-api/api-snapshots/ReactCommonDebugCxx.api
@@ -3892,6 +3892,7 @@ struct facebook::react::ViewTransitionModule::AnimationKeyFrameView {
   public facebook::react::SurfaceId surfaceId;
   public facebook::react::Tag tag;
   public facebook::react::ViewTransitionModule::AnimationKeyFrameViewLayoutMetrics layoutMetrics;
+  public uint32_t transitionId;
 }
 
 struct facebook::react::ViewTransitionModule::AnimationKeyFrameViewLayoutMetrics {
diff --git a/scripts/cxx-api/api-snapshots/ReactCommonNewarchCxx.api b/scripts/cxx-api/api-snapshots/ReactCommonNewarchCxx.api
index 81705abe51bd..e9700e2725df 100644
--- a/scripts/cxx-api/api-snapshots/ReactCommonNewarchCxx.api
+++ b/scripts/cxx-api/api-snapshots/ReactCommonNewarchCxx.api
@@ -3758,6 +3758,7 @@ struct facebook::react::ViewTransitionModule::AnimationKeyFrameView {
   public facebook::react::SurfaceId surfaceId;
   public facebook::react::Tag tag;
   public facebook::react::ViewTransitionModule::AnimationKeyFrameViewLayoutMetrics layoutMetrics;
+  public uint32_t transitionId;
 }
 
 struct facebook::react::ViewTransitionModule::AnimationKeyFrameViewLayoutMetrics {
diff --git a/scripts/cxx-api/api-snapshots/ReactCommonReleaseCxx.api b/scripts/cxx-api/api-snapshots/ReactCommonReleaseCxx.api
index 29810fb16f09..bf1acdc6eb1a 100644
--- a/scripts/cxx-api/api-snapshots/ReactCommonReleaseCxx.api
+++ b/scripts/cxx-api/api-snapshots/ReactCommonReleaseCxx.api
@@ -3883,6 +3883,7 @@ struct facebook::react::ViewTransitionModule::AnimationKeyFrameView {
   public facebook::react::SurfaceId surfaceId;
   public facebook::react::Tag tag;
   public facebook::react::ViewTransitionModule::AnimationKeyFrameViewLayoutMetrics layoutMetrics;
+  public uint32_t transitionId;
 }
 
 struct facebook::react::ViewTransitionModule::AnimationKeyFrameViewLayoutMetrics {