diff --git a/com.unity.netcode.gameobjects/CHANGELOG.md b/com.unity.netcode.gameobjects/CHANGELOG.md
index cb36aa3858..aec4867142 100644
--- a/com.unity.netcode.gameobjects/CHANGELOG.md
+++ b/com.unity.netcode.gameobjects/CHANGELOG.md
@@ -22,6 +22,7 @@ Additional documentation and release notes are available at [Multiplayer Documen
 
 ### Fixed
 
+- Fixed issue where scenes additively loaded before a session started were tracked as loaded on the server but had no scene handle entries, which caused `NetworkSceneManager.UnloadScene` to log an error and leave the scene registered as loaded even though it unloaded on all peers. (#4145)
 - Issue where `NetworkTransform` interpolated towards a point in time taken from the local clock rather than the server clock that state updates are stamped on, which starved the interpolator on clients and reduced interpolation to snapping between state updates. (#4133)
 - Issue where `NetworkTransform.GetTickLatencyInSeconds` returned an absolute network timestamp that grew for as long as the session ran, rather than the tick latency as a duration in seconds that it is documented to return. (#4133)
 - Issue where lerp smoothing was applied per frame instead of over time, which caused the `Lerp` and `SmoothDampening` interpolation types to smooth by different amounts at different frame rates. Results at 60fps are unchanged. (#4130)
diff --git a/com.unity.netcode.gameobjects/Runtime/SceneManagement/NetworkSceneManager.cs b/com.unity.netcode.gameobjects/Runtime/SceneManagement/NetworkSceneManager.cs
index e3a5d2cfe4..c7ae07164f 100644
--- a/com.unity.netcode.gameobjects/Runtime/SceneManagement/NetworkSceneManager.cs
+++ b/com.unity.netcode.gameobjects/Runtime/SceneManagement/NetworkSceneManager.cs
@@ -847,7 +847,7 @@ internal NetworkSceneManager(NetworkManager networkManager)
                 for (int i = 0; i < SceneManager.sceneCount; i++)
                 {
                     var loadedScene = SceneManager.GetSceneAt(i);
-                    ScenesLoaded.Add(loadedScene.handle, loadedScene);
+                    UpdateServerClientSceneHandle(loadedScene.handle, loadedScene.handle, loadedScene);
                 }
                 SceneManagerHandler.PopulateLoadedScenes(ref ScenesLoaded, NetworkManager);
             }
diff --git a/com.unity.netcode.gameobjects/Tests/Runtime/TestHelpers/NetcodeIntegrationTestHelpers.cs b/com.unity.netcode.gameobjects/Tests/Runtime/TestHelpers/NetcodeIntegrationTestHelpers.cs
index 99c7f47afc..7abe3dd19e 100644
--- a/com.unity.netcode.gameobjects/Tests/Runtime/TestHelpers/NetcodeIntegrationTestHelpers.cs
+++ b/com.unity.netcode.gameobjects/Tests/Runtime/TestHelpers/NetcodeIntegrationTestHelpers.cs
@@ -540,7 +540,9 @@ private static void SceneManagerValidationAndTestRunnerInitialization(NetworkMan
                     }
                     return;
                 }
-                networkManager.SceneManager.ServerSceneHandleToClientSceneHandle.Add(scene.handle, scene.handle);
+
+                // The server already registers every scene loaded prior to startup, so only add the test runner scene if it is not already there.
+                networkManager.SceneManager.ServerSceneHandleToClientSceneHandle.TryAdd(scene.handle, scene.handle);
             }
         }
 
diff --git a/testproject/Assets/Tests/Runtime/NetworkSceneManager/NetworkSceneManagerStartupTests.cs b/testproject/Assets/Tests/Runtime/NetworkSceneManager/NetworkSceneManagerStartupTests.cs
index 28cd0b49d2..968f63e9dc 100644
--- a/testproject/Assets/Tests/Runtime/NetworkSceneManager/NetworkSceneManagerStartupTests.cs
+++ b/testproject/Assets/Tests/Runtime/NetworkSceneManager/NetworkSceneManagerStartupTests.cs
@@ -21,6 +21,7 @@ internal class NetworkSceneManagerStartupTests : NetcodeIntegrationTest
     {
         private const string k_ActiveScene = "SessionSynchronize";
         private const string k_AdditionalScene = "InSceneNetworkObjectMovesToDDOL";
+        private const string k_PreLoadedScene = "EmptyScene1";
 
         private readonly List<NetworkObject> m_ObjectsInScenes = new List<NetworkObject>();
         private Scene m_OriginalActiveScene;
@@ -141,6 +142,35 @@ public IEnumerator AllExistingObjectsAreSpawnedAtStartup([Values] LoadSceneMode
             AssertOnTimeout("Timed out waiting for objects to spawn on all clients!");
         }
 
+        /// <summary>
+        /// Validates that a scene additively loaded before the session started is tracked well enough
+        /// to be unloaded through <see cref="NetworkSceneManager"/> without error.
+        /// </summary>
+        [UnityTest]
+        public IEnumerator UnloadPreLoadedScene()
+        {
+            yield return PreLoadScene(k_PreLoadedScene);
+            var preLoadedScene = m_SceneLoaded;
+
+            m_CanStart = true;
+            yield return StartServerAndClients();
+
+            // Scenes loaded before the session started are registered in both the loaded scenes and the
+            // scene handle tables, otherwise unloading them fails part way through and leaks the entry.
+            var sceneManager = GetAuthorityNetworkManager().SceneManager;
+            Assert.IsTrue(sceneManager.ScenesLoaded.ContainsKey(preLoadedScene.handle), $"{k_PreLoadedScene} is not in {nameof(NetworkSceneManager.ScenesLoaded)}!");
+            Assert.IsTrue(sceneManager.ServerSceneHandleToClientSceneHandle.ContainsKey(preLoadedScene.handle), $"{k_PreLoadedScene} is not in {nameof(NetworkSceneManager.ServerSceneHandleToClientSceneHandle)}!");
+
+            var status = sceneManager.UnloadScene(preLoadedScene);
+            Assert.AreEqual(SceneEventProgressStatus.Started, status, $"{nameof(NetworkSceneManager.UnloadScene)} returned {status}!");
+
+            yield return WaitForConditionOrTimeOut(() => !preLoadedScene.isLoaded);
+            AssertOnTimeout($"Timed out waiting for {k_PreLoadedScene} to unload!");
+
+            Assert.IsFalse(sceneManager.ScenesLoaded.ContainsKey(preLoadedScene.handle), $"{k_PreLoadedScene} was unloaded but is still in {nameof(NetworkSceneManager.ScenesLoaded)}!");
+            Assert.IsFalse(sceneManager.ServerSceneHandleToClientSceneHandle.ContainsKey(preLoadedScene.handle), $"{k_PreLoadedScene} was unloaded but is still in {nameof(NetworkSceneManager.ServerSceneHandleToClientSceneHandle)}!");
+        }
+
         #region Scene loading and related methods
 
         /// <summary>