diff --git a/com.unity.netcode.gameobjects/CHANGELOG.md b/com.unity.netcode.gameobjects/CHANGELOG.md
index 85157fe510..65db23ecf2 100644
--- a/com.unity.netcode.gameobjects/CHANGELOG.md
+++ b/com.unity.netcode.gameobjects/CHANGELOG.md
@@ -29,6 +29,7 @@ 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. (#4146)
 - Issue with not being able to spawn initially disabled in-scene placed objects. (#4093)
 - Issue with pre-instantiated network prefab instances being marked as in-scene placed. Now pre-instantiated network prefabs are dynamically spawned. (#4093)
 - Issue where a user could spawn runtime created `NetworkObject` that has a GlobalObjectIdHash of zero. These are not valid instances and will no longer be allowed to spawn. (#4093)
diff --git a/com.unity.netcode.gameobjects/Runtime/SceneManagement/NetworkSceneManager.cs b/com.unity.netcode.gameobjects/Runtime/SceneManagement/NetworkSceneManager.cs
index b0db598848..15f8b5afe4 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 8f32fc1916..02b2503fbd 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>