diff --git a/Source/Core/WinUpdater/WinUI.cpp b/Source/Core/WinUpdater/WinUI.cpp
index 97f2da459b..f6b0a7345c 100644
--- a/Source/Core/WinUpdater/WinUI.cpp
+++ b/Source/Core/WinUpdater/WinUI.cpp
@@ -12,6 +12,8 @@
 #include <ShObjIdl.h>
 #include <shellapi.h>
 
+#include "Common/Event.h"
+#include "Common/ScopeGuard.h"
 #include "Common/StringUtil.h"
 
 namespace
@@ -23,6 +25,7 @@ HWND current_progressbar_handle = nullptr;
 ITaskbarList3* taskbar_list = nullptr;
 
 std::thread ui_thread;
+Common::Event window_created_event;
 
 int GetWindowHeight(HWND hwnd)
 {
@@ -45,7 +48,7 @@ LRESULT CALLBACK WindowProc(HWND hwnd, UINT uMsg, WPARAM wParam, LPARAM lParam)
 };  // namespace
 
 constexpr int PROGRESSBAR_FLAGS = WS_VISIBLE | WS_CHILD | PBS_SMOOTH | PBS_SMOOTHREVERSE;
-constexpr int WINDOW_FLAGS = WS_VISIBLE | WS_CLIPCHILDREN;
+constexpr int WINDOW_FLAGS = WS_CLIPCHILDREN;
 constexpr int PADDING_HEIGHT = 5;
 
 namespace UI
@@ -54,6 +57,9 @@ bool InitWindow()
 {
   InitCommonControls();
 
+  // Notify main thread we're done creating the window when we return
+  Common::ScopeGuard ui_guard{[] { window_created_event.Set(); }};
+
   WNDCLASS wndcl = {};
   wndcl.lpfnWndProc = WindowProc;
   wndcl.hbrBackground = GetSysColorBrush(COLOR_MENU);
@@ -226,6 +232,9 @@ void MessageLoop()
 void Init()
 {
   ui_thread = std::thread(MessageLoop);
+
+  // Wait for UI thread to finish creating the window (or at least attempting to)
+  window_created_event.Wait();
 }
 
 void Stop()