diff --git a/docs/PluginDevelopment.md b/docs/PluginDevelopment.md
index 0a6d7127..689ed841 100644
--- a/docs/PluginDevelopment.md
+++ b/docs/PluginDevelopment.md
@@ -390,7 +390,7 @@ model for FPGA workflows. It is designed to be extended by plugins.
 - Project files use JSON via `UniversalProjectProperties`. Keys are case-insensitive and stored in
   the project file. Common keys:
   - `include` / `exclude`: arrays of glob-like patterns used by `IsPathIncluded`.
-  - `topEntity`: name of the top-level entity or module within `topEntityFile`. Old files that stored a file path in `topEntity` are migrated automatically on load.
+  - `topEntity`: name of the top-level entity or module. The file that contains it is resolved by scanning the project's HDL files (see `FpgaService.GetAllTopEntitiesAsync`). It can be set from the project settings or via the **Set Top Entity** context menu entry on an HDL file in the project explorer. Old files that stored a file path in `topEntity` are migrated automatically on load.
   - `toolchain`: toolchain ID to run on compile.
   - `loader`: loader ID to use for programming.
   - `board`: selected hardware board (evaluation board) name. The legacy key `fpga` is automatically migrated to `board` on load.
@@ -399,7 +399,7 @@ model for FPGA workflows. It is designed to be extended by plugins.
 
 `UniversalFpgaProjectRoot` also registers project entry modification handlers to update:
 - Test bench overlays.
-- Top entity overlays.
+- Top entity overlays (marks the file that contains the current `topEntity`).
 - Reduced opacity for compile-excluded files.
 
 Project-specific files:
diff --git a/src/OneWare.ProjectSystem/Models/UniversalProjectRoot.cs b/src/OneWare.ProjectSystem/Models/UniversalProjectRoot.cs
index 1d001f3a..d5447f42 100644
--- a/src/OneWare.ProjectSystem/Models/UniversalProjectRoot.cs
+++ b/src/OneWare.ProjectSystem/Models/UniversalProjectRoot.cs
@@ -54,6 +54,28 @@ public void InvalidateModifications(IProjectEntry entry)
         _entryModificationHandlers.ForEach(handler => handler(entry));
     }
 
+    /// <summary>
+    /// Re-runs all registered entry modifications for every loaded entry in the project.
+    /// Useful when a project wide state (e.g. the top entity) changes and the affected
+    /// entries are not known upfront.
+    /// </summary>
+    public void InvalidateAllModifications()
+    {
+        foreach (var entry in EnumerateLoadedEntries(this))
+            InvalidateModifications(entry);
+    }
+
+    private static IEnumerable<IProjectEntry> EnumerateLoadedEntries(IProjectExplorerNode node)
+    {
+        if (node.Children == null) yield break;
+
+        foreach (var child in node.Children)
+        {
+            if (child is IProjectEntry entry) yield return entry;
+            foreach (var descendant in EnumerateLoadedEntries(child)) yield return descendant;
+        }
+    }
+
     public Task<bool> LoadAsync(IEnumerable<ProjectPropertyMigration>? migrations = null)
     {
         return Properties.LoadAsync(ProjectFilePath, migrations);
diff --git a/src/OneWare.UniversalFpgaProjectSystem/Models/UniversalFpgaProjectRoot.cs b/src/OneWare.UniversalFpgaProjectSystem/Models/UniversalFpgaProjectRoot.cs
index f4adc048..82aa280e 100644
--- a/src/OneWare.UniversalFpgaProjectSystem/Models/UniversalFpgaProjectRoot.cs
+++ b/src/OneWare.UniversalFpgaProjectSystem/Models/UniversalFpgaProjectRoot.cs
@@ -34,6 +34,19 @@ public UniversalFpgaProjectRoot(string projectFilePath) : base(projectFilePath)
                 x.Icon?.RemoveOverlay("TestBench");
             }
         });
+
+        RegisterProjectEntryModification(x =>
+        {
+            if (x is IProjectFile file && TopEntityFilePath != null &&
+                file.RelativePath.EqualPaths(TopEntityFilePath))
+            {
+                x.Icon?.AddOverlay("TopEntity", "VsImageLib2019.DownloadOverlay16X");
+            }
+            else
+            {
+                x.Icon?.RemoveOverlay("TopEntity");
+            }
+        });
         
         RegisterProjectEntryModification(x =>
         {
@@ -60,6 +73,22 @@ public string? TopEntity
         set => Properties.SetString("topEntity", value);
     }
 
+    /// <summary>
+    /// Relative path of the file that contains the current <see cref="TopEntity"/>.
+    /// This is a runtime-only cache (not persisted) and is used to display the top entity
+    /// indicator on the file that contains the top-level entity.
+    /// </summary>
+    public string? TopEntityFilePath
+    {
+        get;
+        set
+        {
+            if (field == value) return;
+            field = value;
+            InvalidateAllModifications();
+        }
+    }
+
     public string? Toolchain
     {
         get => Properties.GetString("toolchain");
diff --git a/src/OneWare.UniversalFpgaProjectSystem/UniversalFpgaProjectManager.cs b/src/OneWare.UniversalFpgaProjectSystem/UniversalFpgaProjectManager.cs
index 7cef45eb..952fd697 100644
--- a/src/OneWare.UniversalFpgaProjectSystem/UniversalFpgaProjectManager.cs
+++ b/src/OneWare.UniversalFpgaProjectSystem/UniversalFpgaProjectManager.cs
@@ -1,4 +1,6 @@
-using CommunityToolkit.Mvvm.Input;
+using System.Collections.ObjectModel;
+using CommunityToolkit.Mvvm.Input;
+using OneWare.Essentials.Extensions;
 using OneWare.Essentials.Models;
 using OneWare.Essentials.Services;
 using OneWare.UniversalFpgaProjectSystem.Models;
@@ -43,7 +45,15 @@ public UniversalFpgaProjectManager(IProjectExplorerService projectExplorerServic
         }
 
         await root.InitializeAsync();
-        
+
+        await UpdateTopEntityFilePathAsync(root);
+
+        root.Properties.ProjectPropertyChanged += (_, args) =>
+        {
+            if (args.PropertyName.Equals("topEntity", StringComparison.OrdinalIgnoreCase))
+                _ = UpdateTopEntityFilePathAsync(root);
+        };
+
         return root;
     }
 
@@ -54,6 +64,8 @@ public async Task ReloadProjectAsync(IProjectRoot project)
         await root.LoadAsync(_fpgaService.ProjectPropertyMigrations);
         await MigrateLegacyTopEntityAsync(root);
         await root.InitializeAsync();
+
+        await UpdateTopEntityFilePathAsync(root);
         
         //TODO reload open files
         var filesOpenInProject = _mainDockService.OpenFiles
@@ -183,6 +195,15 @@ private void ConstructContextMenu(IReadOnlyList<IProjectExplorerNode> selected,
                 case FpgaProjectFile { Root: UniversalFpgaProjectRoot universalFpgaProjectRoot } file:
                     if (file.Extension is ".vhd" or ".vhdl" or ".v" or ".sv")
                     {
+                        //Set Top Entity
+                        var setTopEntityMenu = new MenuItemModel("SetTopEntity")
+                        {
+                            Header = "Set Top Entity",
+                            Icon = new IconModel("VsImageLib.StartWithoutDebug16X"),
+                            Items = new ObservableCollection<MenuItemModel>()
+                        };
+                        menuItems.Add(setTopEntityMenu);
+                        _ = PopulateTopEntityMenuItemsAsync(setTopEntityMenu, file, universalFpgaProjectRoot);
 
                         //Exclude from compile
                         if (!universalFpgaProjectRoot.IsCompileExcluded(file.RelativePath))
@@ -235,6 +256,62 @@ private void ConstructContextMenu(IReadOnlyList<IProjectExplorerNode> selected,
             }
     }
 
+    private async Task PopulateTopEntityMenuItemsAsync(MenuItemModel menu, IProjectFile file,
+        UniversalFpgaProjectRoot root)
+    {
+        var nodeProvider = _fpgaService.GetNodeProviderByExtension(file.Extension);
+        if (nodeProvider == null) return;
+
+        List<string> entities;
+        try
+        {
+            entities = (await nodeProvider.ExtractTopEntitiesAsync(file)).ToList();
+        }
+        catch
+        {
+            return;
+        }
+
+        if (menu.Items == null) return;
+
+        foreach (var entity in entities)
+        {
+            var entityName = entity;
+            var isCurrent = root.TopEntity == entityName &&
+                            root.TopEntityFilePath != null &&
+                            file.RelativePath.EqualPaths(root.TopEntityFilePath);
+
+            menu.Items.Add(new MenuItemModel(entityName)
+            {
+                Header = entityName,
+                Icon = isCurrent ? new IconModel("BoxIcons.RegularCheck") : null,
+                Command = new RelayCommand(() =>
+                {
+                    root.TopEntity = entityName;
+                    root.TopEntityFilePath = file.RelativePath;
+                    _ = SaveProjectAsync(root);
+                })
+            });
+        }
+    }
+
+    /// <summary>
+    /// Recomputes <see cref="UniversalFpgaProjectRoot.TopEntityFilePath"/> by locating the file
+    /// that contains the current <see cref="UniversalFpgaProjectRoot.TopEntity"/>.
+    /// </summary>
+    private async Task UpdateTopEntityFilePathAsync(UniversalFpgaProjectRoot root)
+    {
+        if (string.IsNullOrEmpty(root.TopEntity))
+        {
+            root.TopEntityFilePath = null;
+            return;
+        }
+
+        var allEntities = await _fpgaService.GetAllTopEntitiesAsync(root);
+        var match = allEntities.FirstOrDefault(x => x.TopEntity == root.TopEntity);
+        root.TopEntityFilePath = match?.File.RelativePath;
+    }
+
     private async Task OpenProjectSettingsDialogAsync(UniversalFpgaProjectRoot root)
     {
         // UniversalFpgaProjectRoot root