diff --git a/scene/main/viewport.cpp b/scene/main/viewport.cpp
index d405fd90903..ae329e1e9cf 100644
--- a/scene/main/viewport.cpp
+++ b/scene/main/viewport.cpp
@@ -184,6 +184,7 @@ public:
 Viewport::GUI::GUI() {
 	dragging = false;
 	drag_successful = false;
+	mouse_in_window = true;
 	mouse_focus = nullptr;
 	mouse_click_grabber = nullptr;
 	mouse_focus_mask = 0;
@@ -398,21 +399,26 @@ void Viewport::_notification(int p_what) {
 				_process_picking(false);
 			}
 		} break;
-		case SceneTree::NOTIFICATION_WM_MOUSE_EXIT: {
-			_drop_physics_mouseover();
-
-			// Unlike on loss of focus (NOTIFICATION_WM_WINDOW_FOCUS_OUT), do not
-			// drop the gui mouseover here, as a scrollbar may be dragged while the
-			// mouse is outside the window (without the window having lost focus).
-			// See bug #39634
+		case NOTIFICATION_WM_MOUSE_ENTER: {
+			gui.mouse_in_window = true;
 		} break;
-		case SceneTree::NOTIFICATION_WM_FOCUS_OUT: {
+		case NOTIFICATION_WM_MOUSE_EXIT: {
+			gui.mouse_in_window = false;
+			_drop_physics_mouseover();
+			_drop_mouse_over();
+			// When the mouse exits the window, we want to end mouse_over, but
+			// not mouse_focus, because, for example, we want to continue
+			// dragging a scrollbar even if the mouse has left the window.
+		} break;
+		case NOTIFICATION_WM_FOCUS_OUT: {
 			_drop_physics_mouseover();
-
 			if (gui.mouse_focus) {
-				//if mouse is being pressed, send a release event
 				_drop_mouse_focus();
 			}
+			// When the window focus changes, we want to end mouse_focus, but
+			// not the mouse_over. Note: The OS will trigger a separate mouse
+			// exit event if the change in focus results in the mouse exiting
+			// the window.
 		} break;
 	}
 }
@@ -1861,9 +1867,6 @@ void Viewport::_gui_input_event(Ref<InputEvent> p_event) {
 
 	if (mb.is_valid()) {
 		gui.key_event_accepted = false;
-
-		Control *over = nullptr;
-
 		Point2 mpos = mb->get_position();
 		if (mb->is_pressed()) {
 			Size2 pos = mpos;
@@ -2057,6 +2060,8 @@ void Viewport::_gui_input_event(Ref<InputEvent> p_event) {
 			// it is different, rather than wait for it to be updated the next time the
 			// mouse is moved, notify the control so that it can e.g. drop the highlight.
 			// This code is duplicated from the mm.is_valid()-case further below.
+
+			Control *over = nullptr;
 			if (gui.mouse_focus) {
 				over = gui.mouse_focus;
 			} else {
@@ -2087,8 +2092,6 @@ void Viewport::_gui_input_event(Ref<InputEvent> p_event) {
 
 		gui.last_mouse_pos = mpos;
 
-		Control *over = nullptr;
-
 		// D&D
 		if (!gui.drag_attempted && gui.mouse_focus && mm->get_button_mask() & BUTTON_MASK_LEFT) {
 			gui.drag_accum += mm->get_relative();
@@ -2135,12 +2138,10 @@ void Viewport::_gui_input_event(Ref<InputEvent> p_event) {
 			}
 		}
 
-		// These sections of code are reused in the mb.is_valid() case further up
-		// for the purpose of notifying controls about potential changes in focus
-		// when the mousebutton is released.
+		Control *over = nullptr;
 		if (gui.mouse_focus) {
 			over = gui.mouse_focus;
-		} else {
+		} else if (gui.mouse_in_window) {
 			over = _gui_find_control(mpos);
 		}
 
@@ -2187,11 +2188,10 @@ void Viewport::_gui_input_event(Ref<InputEvent> p_event) {
 
 			if (over) {
 				_gui_call_notification(over, Control::NOTIFICATION_MOUSE_ENTER);
+				gui.mouse_over = over;
 			}
 		}
 
-		gui.mouse_over = over;
-
 		Control *drag_preview = _gui_get_drag_preview();
 		if (drag_preview) {
 			drag_preview->set_position(mpos);
diff --git a/scene/main/viewport.h b/scene/main/viewport.h
index 8d1de3dfa80..500b46bde7f 100644
--- a/scene/main/viewport.h
+++ b/scene/main/viewport.h
@@ -295,6 +295,7 @@ private:
 		// info used when this is a window
 
 		bool key_event_accepted;
+		bool mouse_in_window;
 		Control *mouse_focus;
 		Control *last_mouse_focus;
 		Control *mouse_click_grabber;