diff --git a/pcsx2-qt/Debugger/DebuggerWindow.cpp b/pcsx2-qt/Debugger/DebuggerWindow.cpp
index f28547ae99f66..6e9a0ab6c5cca 100644
--- a/pcsx2-qt/Debugger/DebuggerWindow.cpp
+++ b/pcsx2-qt/Debugger/DebuggerWindow.cpp
@@ -42,11 +42,17 @@ DebuggerWindow::DebuggerWindow(QWidget* parent)
 	connect(m_ui.actionStepInto, &QAction::triggered, this, &DebuggerWindow::onStepInto);
 	connect(m_ui.actionStepOver, &QAction::triggered, this, &DebuggerWindow::onStepOver);
 	connect(m_ui.actionStepOut, &QAction::triggered, this, &DebuggerWindow::onStepOut);
+	connect(m_ui.actionOnTop, &QAction::triggered, [this] { this->setWindowFlags(this->windowFlags() ^ Qt::WindowStaysOnTopHint); this->show(); });
 
 	connect(g_emu_thread, &EmuThread::onVMPaused, this, &DebuggerWindow::onVMStateChanged);
 	connect(g_emu_thread, &EmuThread::onVMResumed, this, &DebuggerWindow::onVMStateChanged);
 
 	onVMStateChanged(); // If we missed a state change while we weren't loaded
+	
+	// We can't do this in the designer, but we want to right align the actionOnTop action in the toolbar
+	QWidget* spacer = new QWidget(this);
+	spacer->setSizePolicy(QSizePolicy::Expanding, QSizePolicy::Expanding);
+	m_ui.toolBar->insertWidget(m_ui.actionOnTop, spacer);
 
 	m_cpuWidget_r5900 = new CpuWidget(this, r5900Debug);
 	m_cpuWidget_r3000 = new CpuWidget(this, r3000Debug);
diff --git a/pcsx2-qt/Debugger/DebuggerWindow.ui b/pcsx2-qt/Debugger/DebuggerWindow.ui
index ac1aabe1c268f..71a692187ca0c 100644
--- a/pcsx2-qt/Debugger/DebuggerWindow.ui
+++ b/pcsx2-qt/Debugger/DebuggerWindow.ui
@@ -13,6 +13,11 @@
   <property name="windowTitle">
    <string>PCSX2 Debugger</string>
   </property>
+  <property name="windowIcon">
+   <iconset>
+    <normalon>:/icons/AppIcon64.png</normalon>
+   </iconset>
+  </property>
   <widget class="QWidget" name="centralwidget">
    <layout class="QGridLayout" name="gridLayout">
     <item row="0" column="0">
@@ -46,6 +51,7 @@
    <addaction name="actionStepInto"/>
    <addaction name="actionStepOver"/>
    <addaction name="actionStepOut"/>
+   <addaction name="actionOnTop"/>
   </widget>
   <action name="actionRun">
    <property name="icon">
@@ -88,6 +94,17 @@
     <string>Shift+F11</string>
    </property>
   </action>
+  <action name="actionOnTop">
+   <property name="checkable">
+    <bool>true</bool>
+   </property>
+   <property name="text">
+    <string>Always On Top</string>
+   </property>
+   <property name="toolTip">
+    <string>Show this window on top</string>
+   </property>
+  </action>
  </widget>
  <resources/>
  <connections/>
diff --git a/pcsx2-qt/MainWindow.cpp b/pcsx2-qt/MainWindow.cpp
index cb718dba7c44b..cc68ba0e99023 100644
--- a/pcsx2-qt/MainWindow.cpp
+++ b/pcsx2-qt/MainWindow.cpp
@@ -118,6 +118,13 @@ MainWindow::~MainWindow()
 	// make sure the game list isn't refreshing, because it's on a separate thread
 	cancelGameListRefresh();
 
+	if (m_debugger_window)
+	{
+		m_debugger_window->close();
+		m_debugger_window->deleteLater();
+		m_debugger_window = nullptr;
+	}
+
 	// we compare here, since recreate destroys the window later
 	if (g_main_window == this)
 		g_main_window = nullptr;
@@ -2300,7 +2307,8 @@ void MainWindow::doSettings(const char* category /* = nullptr */)
 DebuggerWindow* MainWindow::getDebuggerWindow()
 {
 	if (!m_debugger_window)
-		m_debugger_window = new DebuggerWindow(this);
+		// Don't pass us (this) as the parent, otherwise the window is always on top of the mainwindow (on windows at least)
+		m_debugger_window = new DebuggerWindow(nullptr);
 
 	return m_debugger_window;
 }