diff --git a/CMakeLists.txt b/CMakeLists.txt
index e2d7d2222e..d3cdc937a0 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -232,7 +232,8 @@ endif()
 
 add_definitions(-DUSING_GENERATED_CONFIG_H)
 # General includes
-include_directories(${SDL2_BINARY_DIR}/include ${SDL2_SOURCE_DIR}/include ${SDL2_SOURCE_DIR}/src/video/khronos)
+include_directories(${SDL2_BINARY_DIR}/include ${SDL2_SOURCE_DIR}/include)
+set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -idirafter ${SDL2_SOURCE_DIR}/src/video/khronos")
 
 # All these ENABLED_BY_DEFAULT vars will default to ON if not specified, so
 #  you only need to have a platform override them if they are disabling.
diff --git a/configure b/configure
index b2ca59c89b..18096ae8a4 100755
--- a/configure
+++ b/configure
@@ -15677,7 +15677,7 @@ case "$host" in
         ;;
 esac
 
-INCLUDE="-I$srcdir/include -I$srcdir/src/video/khronos"
+INCLUDE="-I$srcdir/include -idirafter $srcdir/src/video/khronos"
 if test x$srcdir != x.; then
     INCLUDE="-Iinclude $INCLUDE"
 elif test -d .hg; then
diff --git a/configure.in b/configure.in
index 6438126a7a..bb61002902 100644
--- a/configure.in
+++ b/configure.in
@@ -68,7 +68,7 @@ case "$host" in
 esac
 
 dnl Set up the compiler and linker flags
-INCLUDE="-I$srcdir/include -I$srcdir/src/video/khronos"
+INCLUDE="-I$srcdir/include -idirafter $srcdir/src/video/khronos"
 if test x$srcdir != x.; then
     INCLUDE="-Iinclude $INCLUDE"
 elif test -d .hg; then