diff --git a/osu.Framework/Input/Handlers/INeedsMousePositionFeedback.cs b/osu.Framework/Input/Handlers/INeedsMousePositionFeedback.cs
index d98eaf1bea..1111210fdb 100644
--- a/osu.Framework/Input/Handlers/INeedsMousePositionFeedback.cs
+++ b/osu.Framework/Input/Handlers/INeedsMousePositionFeedback.cs
@@ -14,7 +14,7 @@ public interface INeedsMousePositionFeedback
         /// Receives the final mouse position from an <see cref="InputManager"/>.
         /// </summary>
         /// <param name="position">The final mouse position.</param>
-        /// <param name="isSelfFeedback">Whether the feedback was triggered from this handler.</param>
-        void FeedbackMousePositionChange(Vector2 position, bool isSelfFeedback);
+        /// <param name="handler">A handler that reported the final mouse position.</param>
+        void FeedbackMousePositionChange(Vector2 position, InputHandler handler);
     }
 }
diff --git a/osu.Framework/Input/Handlers/Mouse/MouseHandler.cs b/osu.Framework/Input/Handlers/Mouse/MouseHandler.cs
index aa480152c3..8c815f2c1e 100644
--- a/osu.Framework/Input/Handlers/Mouse/MouseHandler.cs
+++ b/osu.Framework/Input/Handlers/Mouse/MouseHandler.cs
@@ -6,6 +6,7 @@
 using System.Diagnostics;
 using osu.Framework.Bindables;
 using osu.Framework.Extensions.EnumExtensions;
+using osu.Framework.Input.Handlers.Pen;
 using osu.Framework.Input.StateChanges;
 using osu.Framework.Platform;
 using osu.Framework.Statistics;
@@ -137,12 +138,16 @@ public override bool Initialize(GameHost host)
             return true;
         }
 
-        public virtual void FeedbackMousePositionChange(Vector2 position, bool isSelfFeedback)
+        public virtual void FeedbackMousePositionChange(Vector2 position, InputHandler handler)
         {
             if (!Enabled.Value)
                 return;
 
-            if (!isSelfFeedback && isActive.Value)
+            // https://github.com/ppy/osu/issues/31948
+            // Pen malfunctions if MouseHandler tries to move the mouse cursor to pen position on Linux.
+            bool disableUpdatingMousePosition = handler is PenHandler && RuntimeInfo.OS == RuntimeInfo.Platform.Linux && FrameworkEnvironment.UseSDL3;
+
+            if (handler != this && isActive.Value && !disableUpdatingMousePosition)
                 // if another handler has updated the cursor position, handle updating the OS cursor so we can seamlessly revert
                 // to mouse control at any point.
                 window.UpdateMousePosition(position);
diff --git a/osu.Framework/Input/InputManager.cs b/osu.Framework/Input/InputManager.cs
index 87efb4345b..8e039c4c9e 100644
--- a/osu.Framework/Input/InputManager.cs
+++ b/osu.Framework/Input/InputManager.cs
@@ -964,7 +964,7 @@ protected virtual void HandleMousePositionChange(MousePositionChangeEvent e)
             foreach (var h in InputHandlers)
             {
                 if (h.Enabled.Value && h is INeedsMousePositionFeedback handler)
-                    handler.FeedbackMousePositionChange(mouse.Position, h == mouseSource);
+                    handler.FeedbackMousePositionChange(mouse.Position, mouseSource);
             }
 
             handleMouseMove(state, e.LastPosition);
diff --git a/osu.Framework/Platform/Windows/WindowsMouseHandler.cs b/osu.Framework/Platform/Windows/WindowsMouseHandler.cs
index 4abe150a6e..4e3d86714e 100644
--- a/osu.Framework/Platform/Windows/WindowsMouseHandler.cs
+++ b/osu.Framework/Platform/Windows/WindowsMouseHandler.cs
@@ -2,6 +2,7 @@
 // See the LICENCE file in the repository root for full licence text.
 
 using System.Runtime.Versioning;
+using osu.Framework.Input.Handlers;
 using osu.Framework.Input.Handlers.Mouse;
 using osuTK;
 
@@ -31,10 +32,10 @@ public override bool Initialize(GameHost host)
             return base.Initialize(host);
         }
 
-        public override void FeedbackMousePositionChange(Vector2 position, bool isSelfFeedback)
+        public override void FeedbackMousePositionChange(Vector2 position, InputHandler handler)
         {
             window.LastMousePosition = position;
-            base.FeedbackMousePositionChange(position, isSelfFeedback);
+            base.FeedbackMousePositionChange(position, handler);
         }
     }
 }