diff --git a/src/core/frontend/emu_window.cpp b/src/core/frontend/emu_window.cpp
index 2d5dfde54f..cdefdb5414 100644
--- a/src/core/frontend/emu_window.cpp
+++ b/src/core/frontend/emu_window.cpp
@@ -55,15 +55,17 @@ EmuWindow::EmuWindow(bool is_secondary_) : is_secondary{is_secondary_} {
 }
 
 EmuWindow::~EmuWindow() = default;
-/**
- * Check if the given x/y coordinates are within the touchpad specified by the framebuffer layout
- * @param layout FramebufferLayout object describing the framebuffer size and screen positions
- * @param framebuffer_x Framebuffer x-coordinate to check
- * @param framebuffer_y Framebuffer y-coordinate to check
- * @return True if the coordinates are within the touchpad, otherwise false
- */
-static bool IsWithinTouchscreen(const Layout::FramebufferLayout& layout, unsigned framebuffer_x,
-                                unsigned framebuffer_y) {
+
+bool EmuWindow::IsWithinTouchscreen(const Layout::FramebufferLayout& layout, unsigned framebuffer_x,
+                                    unsigned framebuffer_y) {
+#ifndef ANDROID
+    // If separate windows and the touch is in the primary (top) screen, ignore it.
+    if (Settings::values.layout_option.GetValue() == Settings::LayoutOption::SeparateWindows &&
+        !is_secondary && !Settings::values.swap_screen.GetValue()) {
+        return false;
+    }
+#endif
+
     if (Settings::values.render_3d.GetValue() == Settings::StereoRenderOption::SideBySide) {
         return (framebuffer_y >= layout.bottom_screen.top &&
                 framebuffer_y < layout.bottom_screen.bottom &&
diff --git a/src/core/frontend/emu_window.h b/src/core/frontend/emu_window.h
index 26c14ef50c..61b09583b5 100644
--- a/src/core/frontend/emu_window.h
+++ b/src/core/frontend/emu_window.h
@@ -288,6 +288,17 @@ private:
 
     void CreateTouchState();
 
+    /**
+     * Check if the given x/y coordinates are within the touchpad specified by the framebuffer
+     * layout
+     * @param layout FramebufferLayout object describing the framebuffer size and screen positions
+     * @param framebuffer_x Framebuffer x-coordinate to check
+     * @param framebuffer_y Framebuffer y-coordinate to check
+     * @return True if the coordinates are within the touchpad, otherwise false
+     */
+    bool IsWithinTouchscreen(const Layout::FramebufferLayout& layout, unsigned framebuffer_x,
+                             unsigned framebuffer_y);
+
     Layout::FramebufferLayout framebuffer_layout; ///< Current framebuffer layout
 
     WindowConfig config{};        ///< Internal configuration (changes pending for being applied in