diff --git a/Source/Core/DolphinQt/CMakeLists.txt b/Source/Core/DolphinQt/CMakeLists.txt
index 44a59d5313..79e5cce207 100644
--- a/Source/Core/DolphinQt/CMakeLists.txt
+++ b/Source/Core/DolphinQt/CMakeLists.txt
@@ -462,6 +462,7 @@ if(WIN32)
 
   # Copy Sys dir
   add_custom_command(TARGET dolphin-emu POST_BUILD
+    COMMAND ${CMAKE_COMMAND} -E remove_directory "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/Sys"
     COMMAND ${CMAKE_COMMAND} -E copy_directory "${CMAKE_SOURCE_DIR}/Data/Sys" "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/Sys"
   )
 
diff --git a/Source/Core/DolphinQt/DolphinQt.vcxproj b/Source/Core/DolphinQt/DolphinQt.vcxproj
index b023262a23..7ee8cac6a5 100644
--- a/Source/Core/DolphinQt/DolphinQt.vcxproj
+++ b/Source/Core/DolphinQt/DolphinQt.vcxproj
@@ -490,6 +490,7 @@
   </ItemGroup>
   <Target Name="AfterBuild" Inputs="@(AllInputFiles)" Outputs="@(AllInputFiles -> '$(BinaryOutputDir)%(RecursiveDir)%(Filename)%(Extension)')">
     <Message Text="Copying Data directory..." Importance="High" />
+    <RemoveDir Directories="$(BinaryOutputDir)Sys" />
     <Copy SourceFiles="@(DataSysFiles)" DestinationFolder="$(BinaryOutputDir)%(RecursiveDir)" SkipUnchangedFiles="True" />
     <Copy SourceFiles="@(DataTxtFiles)" DestinationFolder="$(BinaryOutputDir)" SkipUnchangedFiles="True" />
     <Message Text="Copy: @(BinaryFiles) -&gt; $(BinaryOutputDir)" Importance="High" />