diff --git a/src/components/collapsible_nav/collapsible_nav.spec.tsx b/src/components/collapsible_nav/collapsible_nav.spec.tsx
new file mode 100644
index 00000000000..d32574e0057
--- /dev/null
+++ b/src/components/collapsible_nav/collapsible_nav.spec.tsx
@@ -0,0 +1,83 @@
+/*
+ * Copyright Elasticsearch B.V. and/or licensed to Elasticsearch B.V. under one
+ * or more contributor license agreements. Licensed under the Elastic License
+ * 2.0 and the Server Side Public License, v 1; you may not use this file except
+ * in compliance with, at your election, the Elastic License 2.0 or the Server
+ * Side Public License, v 1.
+ */
+
+/// <reference types="../../../cypress/support"/>
+
+import React, { useState } from 'react';
+
+import { EuiCollapsibleNav } from './collapsible_nav';
+import { EuiHeader, EuiHeaderSectionItemButton } from '../header';
+import { EuiIcon } from '../icon';
+
+const Nav = () => {
+  const [isOpen, setIsOpen] = useState(false);
+
+  return (
+    <EuiHeader
+      style={{ zIndex: 1001 }}
+      position="fixed"
+      sections={[
+        {
+          items: [
+            <EuiCollapsibleNav
+              style={{ top: 48 }}
+              id="navSpec"
+              isOpen={isOpen}
+              button={
+                <EuiHeaderSectionItemButton
+                  data-test-subj="navSpecButton"
+                  aria-label="Toggle main navigation"
+                  onClick={() => setIsOpen(!isOpen)}
+                >
+                  <EuiIcon type={'menu'} size="m" aria-hidden="true" />
+                </EuiHeaderSectionItemButton>
+              }
+              onClose={() => setIsOpen(false)}
+            >
+              <button data-test-subj="itemA">Item A</button>
+              <button data-test-subj="itemB">Item B</button>
+              <button data-test-subj="itemC">Item C</button>
+              <input data-test-subj="itemD" />
+            </EuiCollapsibleNav>,
+          ],
+        },
+      ]}
+    />
+  );
+};
+
+describe('EuiCollapsibleNav', () => {
+  describe('Elastic pattern', () => {
+    describe('Toggle button behavior', () => {
+      it('opens and closes nav when the main button is clicked', () => {
+        cy.mount(<Nav />);
+        cy.wait(400); // Wait for the button to be clickable
+        cy.get('[data-test-subj="navSpecButton"]').realClick();
+        expect(cy.get('#navSpec').should('exist'));
+        cy.get('[data-test-subj="navSpecButton"]').realClick();
+        expect(cy.get('#navSpec').should('not.exist'));
+      });
+
+      it('closes the nav when the overlay mask is clicked', () => {
+        cy.mount(<Nav />);
+        cy.wait(400);
+        cy.get('[data-test-subj="navSpecButton"]').realClick();
+        cy.get('.euiOverlayMask').realClick();
+        expect(cy.get('#navSpec').should('not.exist'));
+      });
+
+      it('closes the nav when the close button is clicked', () => {
+        cy.mount(<Nav />);
+        cy.wait(400);
+        cy.get('[data-test-subj="navSpecButton"]').realClick();
+        cy.get('[data-test-subj="euiFlyoutCloseButton"]').realClick();
+        expect(cy.get('#navSpec').should('not.exist'));
+      });
+    });
+  });
+});
diff --git a/src/components/collapsible_nav/collapsible_nav.tsx b/src/components/collapsible_nav/collapsible_nav.tsx
index 2531f2a5021..ffac8a407e9 100644
--- a/src/components/collapsible_nav/collapsible_nav.tsx
+++ b/src/components/collapsible_nav/collapsible_nav.tsx
@@ -12,6 +12,7 @@ import React, {
   ReactElement,
   ReactNode,
   useEffect,
+  useRef,
   useState,
 } from 'react';
 import classNames from 'classnames';
@@ -19,6 +20,7 @@ import {
   useGeneratedHtmlId,
   isWithinMinBreakpoint,
   throttle,
+  useCombinedRefs,
 } from '../../services';
 import { EuiFlyout, EuiFlyoutProps } from '../flyout';
 
@@ -71,12 +73,19 @@ export const EuiCollapsibleNav: FunctionComponent<EuiCollapsibleNavProps> = ({
   outsideClickCloses = true,
   closeButtonPosition = 'outside',
   paddingSize = 'none',
+  focusTrapProps: _focusTrapProps = {},
   ...rest
 }) => {
   const flyoutID = useGeneratedHtmlId({
     conditionalId: id,
     suffix: 'euiCollapsibleNav',
   });
+  const buttonRef = useRef();
+  const combinedButtonRef = useCombinedRefs([button?.props.ref, buttonRef]);
+  const focusTrapProps: EuiFlyoutProps['focusTrapProps'] = {
+    ..._focusTrapProps,
+    shards: [buttonRef, ...(_focusTrapProps.shards || [])],
+  };
 
   /**
    * Setting the initial state of pushed based on the `type` prop
@@ -136,6 +145,7 @@ export const EuiCollapsibleNav: FunctionComponent<EuiCollapsibleNavProps> = ({
           onMouseUpCapture: (e: React.MouseEvent<HTMLElement>) => {
             e.nativeEvent.stopImmediatePropagation();
           },
+          ref: combinedButtonRef,
         });
 
   const flyout = (
@@ -151,6 +161,7 @@ export const EuiCollapsibleNav: FunctionComponent<EuiCollapsibleNavProps> = ({
       outsideClickCloses={outsideClickCloses}
       closeButtonPosition={closeButtonPosition}
       paddingSize={paddingSize}
+      focusTrapProps={focusTrapProps}
       {...rest}
       // Props dependent on internal docked status
       type={navIsDocked ? 'push' : 'overlay'}
diff --git a/src/components/flyout/flyout.tsx b/src/components/flyout/flyout.tsx
index 79aaa35ad0d..f79f5b5a241 100644
--- a/src/components/flyout/flyout.tsx
+++ b/src/components/flyout/flyout.tsx
@@ -30,7 +30,7 @@ import {
 } from '../../services';
 
 import { CommonProps, keysOf, PropsOfElement } from '../common';
-import { EuiFocusTrap } from '../focus_trap';
+import { EuiFocusTrap, EuiFocusTrapProps } from '../focus_trap';
 import { EuiOverlayMask, EuiOverlayMaskProps } from '../overlay_mask';
 import { EuiButtonIcon, EuiButtonIconPropsForButton } from '../button';
 import { EuiI18n } from '../i18n';
@@ -151,6 +151,12 @@ interface _EuiFlyoutProps {
    */
   pushMinBreakpoint?: EuiBreakpointSize | number;
   style?: CSSProperties;
+  /**
+   * Object of props passed to EuiFocusTrap.
+   * `shards` specifies an array of elements that will be considered part of the flyout, preventing the flyout from being closed when clicked.
+   * `closeOnMouseup` will delay the close callback, allowing time for external toggle buttons to handle close behavior.
+   */
+  focusTrapProps?: Pick<EuiFocusTrapProps, 'closeOnMouseup' | 'shards'>;
 }
 
 const defaultElement = 'div';
@@ -189,6 +195,7 @@ export const EuiFlyout = forwardRef(
       outsideClickCloses,
       role = 'dialog',
       pushMinBreakpoint = 'l',
+      focusTrapProps,
       ...rest
     }: EuiFlyoutProps<T>,
     ref:
@@ -362,6 +369,7 @@ export const EuiFlyout = forwardRef(
         disabled={isPushed}
         clickOutsideDisables={!ownFocus}
         onClickOutside={onClickOutside}
+        {...focusTrapProps}
       >
         <Element
           {...(rest as ComponentPropsWithRef<T>)}
diff --git a/src/components/focus_trap/focus_trap.spec.tsx b/src/components/focus_trap/focus_trap.spec.tsx
index 7687438a486..d8a8988ac9e 100644
--- a/src/components/focus_trap/focus_trap.spec.tsx
+++ b/src/components/focus_trap/focus_trap.spec.tsx
@@ -8,7 +8,7 @@
 
 /// <reference types="../../../cypress/support"/>
 
-import React from 'react';
+import React, { useRef } from 'react';
 import { EuiFocusTrap } from './focus_trap';
 import { EuiPortal } from '../portal';
 
@@ -157,4 +157,80 @@ describe('EuiFocusTrap', () => {
       cy.get('[data-focus-lock-disabled=false]').should('not.exist');
     });
   });
+
+  describe('outside click handling', () => {
+    const Trap = ({
+      onClickOutside,
+      shards,
+      closeOnMouseup,
+    }: {
+      onClickOutside?: any;
+      shards?: boolean;
+      closeOnMouseup?: boolean;
+    }) => {
+      const buttonRef = useRef();
+      return (
+        <div>
+          <EuiFocusTrap
+            onClickOutside={onClickOutside}
+            shards={shards ? [buttonRef] : []}
+            closeOnMouseup={closeOnMouseup}
+          >
+            <div data-test-subj="container">
+              <input data-test-subj="input" />
+              <input data-test-subj="input2" />
+            </div>
+          </EuiFocusTrap>
+          <button ref={buttonRef} data-test-subj="outside">
+            outside the focus trap
+          </button>
+          <button data-test-subj="outside2">also outside the focus trap</button>
+        </div>
+      );
+    };
+
+    it('calls the callback on mousedown', () => {
+      const onClickOutside = cy.stub();
+      cy.mount(<Trap onClickOutside={onClickOutside} />);
+
+      cy.get('[data-test-subj=outside]')
+        .realMouseDown()
+        .then(() => {
+          expect(onClickOutside).to.be.called;
+        });
+    });
+
+    it('calls the callback on mouseup when using closeOnMouseup', () => {
+      const onClickOutside = cy.stub();
+      cy.mount(<Trap onClickOutside={onClickOutside} closeOnMouseup />);
+
+      cy.get('[data-test-subj=outside]')
+        .realMouseDown()
+        .then(() => {
+          expect(onClickOutside).to.not.be.called;
+        });
+      cy.get('[data-test-subj=outside]')
+        .click() // real events not  working here
+        .then(() => {
+          expect(onClickOutside).to.be.called;
+        });
+    });
+
+    it('does not call the callback if the element is a shard', () => {
+      const onClickOutside = cy.stub();
+      cy.mount(<Trap onClickOutside={onClickOutside} shards />);
+
+      cy.get('[data-test-subj=outside]')
+        .realMouseDown()
+        .then(() => {
+          expect(onClickOutside).to.not.be.called;
+        });
+      // But still calls if the element is not a shard
+      cy.get('[data-test-subj=outside2]')
+        .realMouseDown()
+        .then(() => {
+          expect(onClickOutside).to.be.called;
+        });
+    });
+  });
 });
diff --git a/src/components/focus_trap/focus_trap.tsx b/src/components/focus_trap/focus_trap.tsx
index fc67ba70f2b..b210e9f902c 100644
--- a/src/components/focus_trap/focus_trap.tsx
+++ b/src/components/focus_trap/focus_trap.tsx
@@ -16,6 +16,11 @@ import { findElementBySelectorOrRef, ElementTarget } from '../../services';
 export type FocusTarget = ElementTarget;
 
 interface EuiFocusTrapInterface {
+  /**
+   * Whether `onClickOutside` should be called on mouseup instead of mousedown.
+   * This flag can be used to prevent conflicts with outside toggle buttons by delaying the closing click callback.
+   */
+  closeOnMouseup?: boolean;
   /**
    * Clicking outside the trap area will disable the trap
    */
@@ -64,6 +69,10 @@ export class EuiFocusTrap extends Component<EuiFocusTrapProps, State> {
     }
   }
 
+  componentWillUnmount() {
+    this.removeMouseupListener();
+  }
+
   // Programmatically sets focus on a nested DOM node; optional
   setInitialFocus = (initialFocus?: FocusTarget) => {
     const node = findElementBySelectorOrRef(initialFocus);
@@ -72,14 +81,31 @@ export class EuiFocusTrap extends Component<EuiFocusTrapProps, State> {
     node.setAttribute('data-autofocus', 'true');
   };
 
+  onMouseupOutside = (e: MouseEvent | TouchEvent) => {
+    this.removeMouseupListener();
+    // Timeout gives precedence to the consumer to initiate close if it has toggle behavior.
+    // Otherwise this event may occur first and the consumer toggle will reopen the flyout.
+    setTimeout(() => this.props.onClickOutside?.(e));
+  };
+
+  addMouseupListener = () => {
+    document.addEventListener('mouseup', this.onMouseupOutside);
+    document.addEventListener('touchend', this.onMouseupOutside);
+  };
+
+  removeMouseupListener = () => {
+    document.removeEventListener('mouseup', this.onMouseupOutside);
+    document.removeEventListener('touchend', this.onMouseupOutside);
+  };
+
   handleOutsideClick: ReactFocusOnProps['onClickOutside'] = (...args) => {
-    const { onClickOutside, clickOutsideDisables } = this.props;
+    const { onClickOutside, clickOutsideDisables, closeOnMouseup } = this.props;
     if (clickOutsideDisables) {
       this.setState({ hasBeenDisabledByClick: true });
     }
 
     if (onClickOutside) {
-      onClickOutside(...args);
+      closeOnMouseup ? this.addMouseupListener() : onClickOutside(...args);
     }
   };
 
diff --git a/upcoming_changelogs/5860.md b/upcoming_changelogs/5860.md
new file mode 100644
index 00000000000..172fbf6f29f
--- /dev/null
+++ b/upcoming_changelogs/5860.md
@@ -0,0 +1,6 @@
+- Added the `focusTrapProps` prop to `EuiFlyout` to aid outside click detection and closing event
+
+**Bug fixes**
+
+- Fixed `EuiCollapsibleNav` failing to close when the button is clicked
+