diff --git a/lib/lib.rs b/lib/lib.rs
index b04a1488b..b5bba5d87 100644
--- a/lib/lib.rs
+++ b/lib/lib.rs
@@ -266,6 +266,7 @@ pub async fn js_create_graph(
         file_system: &NullFileSystem,
         jsr_url_provider: Default::default(),
         npm_resolver: None,
+        passthrough_jsr_specifiers: false,
         module_analyzer: Default::default(),
         imports,
         reporter: None,
diff --git a/src/graph.rs b/src/graph.rs
index 8457e7c01..8f37b7317 100644
--- a/src/graph.rs
+++ b/src/graph.rs
@@ -1017,6 +1017,10 @@ pub struct BuildOptions<'a> {
   pub executor: &'a dyn Executor,
   pub file_system: &'a dyn FileSystem,
   pub jsr_url_provider: &'a dyn JsrUrlProvider,
+  /// Whether to pass through JSR specifiers to the resolver instead of
+  /// resolving them. This is useful in cases where you want to mark JSR
+  /// specifiers as external.
+  pub passthrough_jsr_specifiers: bool,
   pub module_analyzer: &'a dyn ModuleAnalyzer,
   pub npm_resolver: Option<&'a dyn NpmResolver>,
   pub reporter: Option<&'a dyn Reporter>,
@@ -1447,6 +1451,7 @@ impl ModuleGraph {
       options.is_dynamic,
       options.file_system,
       options.jsr_url_provider,
+      options.passthrough_jsr_specifiers,
       options.resolver,
       options.npm_resolver,
       loader,
@@ -2885,6 +2890,7 @@ struct Builder<'a, 'graph> {
   in_dynamic_branch: bool,
   file_system: &'a dyn FileSystem,
   jsr_url_provider: &'a dyn JsrUrlProvider,
+  passthrough_jsr_specifiers: bool,
   loader: &'a mut dyn Loader,
   resolver: Option<&'a dyn Resolver>,
   npm_resolver: Option<&'a dyn NpmResolver>,
@@ -2907,6 +2913,7 @@ impl<'a, 'graph> Builder<'a, 'graph> {
     is_dynamic: bool,
     file_system: &'a dyn FileSystem,
     jsr_url_provider: &'a dyn JsrUrlProvider,
+    passthrough_jsr_specifiers: bool,
     resolver: Option<&'a dyn Resolver>,
     npm_resolver: Option<&'a dyn NpmResolver>,
     loader: &'a mut dyn Loader,
@@ -2923,6 +2930,7 @@ impl<'a, 'graph> Builder<'a, 'graph> {
       in_dynamic_branch: is_dynamic,
       file_system,
       jsr_url_provider,
+      passthrough_jsr_specifiers,
       loader,
       resolver,
       npm_resolver,
@@ -3624,7 +3632,7 @@ impl<'a, 'graph> Builder<'a, 'graph> {
     }
 
     let maybe_range = maybe_range.map(ToOwned::to_owned);
-    if specifier.scheme() == "jsr" {
+    if !self.passthrough_jsr_specifiers && specifier.scheme() == "jsr" {
       self.load_jsr_specifier(specifier.clone(), maybe_range, is_dynamic);
       return;
     } else if let Some(npm_resolver) = self.npm_resolver {
diff --git a/src/lib.rs b/src/lib.rs
index 4c789932f..624fe2d17 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -4067,4 +4067,54 @@ export function a(a: A): B {
       ModuleGraphError::TypesResolutionError(_)
     ));
   }
+
+  #[tokio::test]
+  async fn test_passthrough_jsr_specifiers() {
+    let mut loader = setup(
+      vec![
+        (
+          "file:///a/test01.ts",
+          Source::Module {
+            specifier: "file:///a/test01.ts",
+            maybe_headers: None,
+            content: r#"import "jsr:@foo/bar@1";"#,
+          },
+        ),
+        ("jsr:@foo/bar@1", Source::External("jsr:@foo/bar@1")),
+      ],
+      vec![],
+    );
+    let root_specifier =
+      ModuleSpecifier::parse("file:///a/test01.ts").expect("bad url");
+    let mut graph = ModuleGraph::new(GraphKind::All);
+    graph
+      .build(
+        vec![root_specifier.clone()],
+        &mut loader,
+        BuildOptions {
+          passthrough_jsr_specifiers: true,
+          ..Default::default()
+        },
+      )
+      .await;
+    assert_eq!(graph.module_slots.len(), 2);
+    assert_eq!(graph.roots, vec![root_specifier.clone()]);
+    assert!(graph.contains(&root_specifier));
+    let module = graph
+      .module_slots
+      .get(&root_specifier)
+      .unwrap()
+      .module()
+      .unwrap()
+      .js()
+      .unwrap();
+    assert_eq!(module.dependencies.len(), 1);
+    let maybe_dependency = module.dependencies.get("jsr:@foo/bar@1");
+    assert!(maybe_dependency.is_some());
+    let dependency_specifier =
+      ModuleSpecifier::parse("jsr:@foo/bar@1").unwrap();
+    let maybe_dep_module_slot = graph.get(&dependency_specifier);
+    let dep_module_slot = maybe_dep_module_slot.unwrap();
+    assert!(dep_module_slot.external().is_some());
+  }
 }