diff --git a/src/libs/Navigation/AppNavigator/AuthScreens.tsx b/src/libs/Navigation/AppNavigator/AuthScreens.tsx
index 4180daa51e23..fcf120df0f03 100644
--- a/src/libs/Navigation/AppNavigator/AuthScreens.tsx
+++ b/src/libs/Navigation/AppNavigator/AuthScreens.tsx
@@ -25,6 +25,7 @@ import useGPSInProgressModal from '@hooks/useGPSInProgressModal';
 import useGPSTripStateChecker from '@hooks/useGPSTripStateChecker';
 import useOnboardingFlowRouter from '@hooks/useOnboardingFlow';
 import useResponsiveLayout from '@hooks/useResponsiveLayout';
+import useRootNavigationState from '@hooks/useRootNavigationState';
 import useShouldSuppressPromotionalUI from '@hooks/useShouldSuppressPromotionalUI';
 import {SidebarOrderedReportsContextProvider} from '@hooks/useSidebarOrderedReports';
 import useStyleUtils from '@hooks/useStyleUtils';
@@ -137,6 +138,8 @@ function AuthScreens() {
     const modalCardStyleInterpolator = useModalCardStyleInterpolator();
     const {isVisitingSecureLink} = useOnboardingFlowRouter();
     const shouldSuppressPromotionalUI = useShouldSuppressPromotionalUI();
+    // Subscribed to navigation state so the onboarding navigator gets registered as soon as the user leaves the validate login screen
+    const shouldHideOnboardingNavigator = useRootNavigationState(Navigation.shouldHideOnboardingNavigator);
     useGPSTripStateChecker();
     useGPSInProgressModal();
 
@@ -356,7 +359,7 @@ function AuthScreens() {
                          * screen in and out of the RootStack mid-session (which resets the navigator's state to its initial
                          * route). OnboardingGuard and useOnboardingFlowRouter gate whether/when a user actually lands here.
                          */}
-                        {!shouldSuppressPromotionalUI && !isVisitingSecureLink && !Navigation.isValidateLoginFlow() && (
+                        {!shouldSuppressPromotionalUI && !isVisitingSecureLink && !shouldHideOnboardingNavigator && (
                             <RootStack.Screen
                                 name={NAVIGATORS.ONBOARDING_MODAL_NAVIGATOR}
                                 options={{...rootNavigatorScreenOptions.basicModalNavigator, gestureEnabled: false}}
diff --git a/src/libs/Navigation/Navigation.ts b/src/libs/Navigation/Navigation.ts
index ad356bac40ab..f52cc4f5c15f 100644
--- a/src/libs/Navigation/Navigation.ts
+++ b/src/libs/Navigation/Navigation.ts
@@ -1127,10 +1127,16 @@ function isOnboardingFlow() {
     return isOnboardingFlowName(currentFocusedRoute?.name);
 }
 
-function isValidateLoginFlow() {
-    const state = navigationRef.getRootState();
-    const currentFocusedRoute = findFocusedRoute(state);
-    return currentFocusedRoute?.name === SCREENS.VALIDATE_LOGIN;
+function isValidateLoginFlow(state: NavigationState | undefined) {
+    return !!state && findFocusedRoute(state)?.name === SCREENS.VALIDATE_LOGIN;
+}
+
+/**
+ * Keeps onboarding from opening over the validate login screen. Once the onboarding navigator is in the root stack it stays
+ * registered, because unregistering it drops its route and the user's onboarding progress.
+ */
+function shouldHideOnboardingNavigator(state: NavigationState | undefined) {
+    return isValidateLoginFlow(state) && !state?.routes.some((route) => route.name === NAVIGATORS.ONBOARDING_MODAL_NAVIGATOR);
 }
 
 function clearPreloadedRoutes() {
@@ -1333,6 +1339,7 @@ export default {
     isOnboardingFlow,
     clearPreloadedRoutes,
     isValidateLoginFlow,
+    shouldHideOnboardingNavigator,
     dismissToPreviousRHP,
     dismissToSuperWideRHP,
     revealRouteBeforeDismissingModal,
diff --git a/tests/navigation/NavigationTests.tsx b/tests/navigation/NavigationTests.tsx
index 1f5f0c787b43..8408641005a8 100644
--- a/tests/navigation/NavigationTests.tsx
+++ b/tests/navigation/NavigationTests.tsx
@@ -4,8 +4,13 @@ import useResponsiveLayout from '@hooks/useResponsiveLayout';
 
 import getIsNarrowLayout from '@libs/getIsNarrowLayout';
 import Navigation from '@libs/Navigation/Navigation';
+import navigationRef from '@libs/Navigation/navigationRef';
 
 import CONST from '@src/CONST';
+import NAVIGATORS from '@src/NAVIGATORS';
+import SCREENS from '@src/SCREENS';
+
+import type {NavigationState} from '@react-navigation/native';
 
 import React from 'react';
 
@@ -19,6 +24,18 @@ jest.mock('@pages/inbox/sidebar/NavigationTabBarAvatar');
 const mockedGetIsNarrowLayout = jest.mocked(getIsNarrowLayout);
 const mockedUseResponsiveLayout = jest.mocked(useResponsiveLayout);
 
+/** Builds a root stack state with the given routes, focused on the last one */
+function buildRootState(routeNames: string[]): NavigationState {
+    return {
+        key: 'root',
+        index: routeNames.length - 1,
+        routeNames,
+        routes: routeNames.map((name) => ({key: `${name}-key`, name})),
+        type: 'stack',
+        stale: false,
+    };
+}
+
 describe('Navigation', () => {
     beforeEach(() => {
         mockedGetIsNarrowLayout.mockReturnValue(false);
@@ -41,7 +58,36 @@ describe('Navigation', () => {
                 />,
             );
 
-            expect(Navigation.isValidateLoginFlow()).toBe(true);
+            expect(Navigation.isValidateLoginFlow(navigationRef.getRootState())).toBe(true);
+        });
+    });
+
+    describe('shouldHideOnboardingNavigator', () => {
+        it('should hide the onboarding navigator on the validate login screen before onboarding has started', () => {
+            // Given a fresh magic link sign-in, where the validate login screen is focused and onboarding isn't in the root stack yet
+            const state = buildRootState([NAVIGATORS.TAB_NAVIGATOR, SCREENS.VALIDATE_LOGIN]);
+
+            // When checking whether the onboarding navigator should be registered
+            // Then it is hidden so onboarding doesn't open over the validate login screen
+            expect(Navigation.shouldHideOnboardingNavigator(state)).toBe(true);
+        });
+
+        it('should keep the onboarding navigator when the validate login screen is pushed over onboarding', () => {
+            // Given a user in the middle of onboarding who opens a magic link, pushing the validate login screen over the onboarding navigator
+            const state = buildRootState([NAVIGATORS.TAB_NAVIGATOR, NAVIGATORS.ONBOARDING_MODAL_NAVIGATOR, SCREENS.VALIDATE_LOGIN]);
+
+            // When checking whether the onboarding navigator should be registered
+            // Then it stays registered, because unregistering it would drop the onboarding route and the user's progress
+            expect(Navigation.shouldHideOnboardingNavigator(state)).toBe(false);
+        });
+
+        it('should not hide the onboarding navigator once the user leaves the validate login screen', () => {
+            // Given the validate login screen was popped and the user is back on the tab navigator
+            const state = buildRootState([NAVIGATORS.TAB_NAVIGATOR]);
+
+            // When checking whether the onboarding navigator should be registered
+            // Then it is registered so startOnboardingFlow can reset into it
+            expect(Navigation.shouldHideOnboardingNavigator(state)).toBe(false);
         });
     });
 });