diff --git a/configure.ac b/configure.ac
index 80f51e09a..ddfbb92d8 100644
--- a/configure.ac
+++ b/configure.ac
@@ -280,7 +280,12 @@ import sys
 print(pathlib.Path(shutil.which(sys.argv@<:@1@:>@) or sys.argv@<:@1@:>@).resolve().parent.parent / "include")
 ' "$LEX")
 if test -f "$flex_include/FlexLexer.h"; then
-   CPPFLAGS="$CPPFLAGS -I$flex_include"
+   if test -n "$MSYSTEM"; then
+      # Search MSYS Flex headers after the active toolchain's system headers.
+      CPPFLAGS="$CPPFLAGS -idirafter $flex_include"
+   else
+      CPPFLAGS="$CPPFLAGS -I$flex_include"
+   fi
 fi
 
 AC_CHECK_PROG(YACC,bison,bison)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 000e63e1d..1d9211f1e 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -565,9 +565,18 @@ set_target_properties(
         MSVC_RUNTIME_LIBRARY MultiThreaded$<IF:$<CONFIG:Release>,,DebugDLL>
         #JOB_POOL_LINK         one_job      # Linking takes lots of resources
         INTERPROCEDURAL_OPTIMIZATION_RELEASE $<IF:MINGW,FALSE,TRUE>
-        INCLUDE_DIRECTORIES ${FLEX_INCLUDE_DIR}
 )
 
+if(MINGW)
+    # Search MSYS Flex headers after the active toolchain's system headers.
+    target_compile_options(
+        ${verilator}
+        PRIVATE -idirafter "${FLEX_INCLUDE_DIR}"
+    )
+else()
+    target_include_directories(${verilator} PRIVATE "${FLEX_INCLUDE_DIR}")
+endif()
+
 add_dependencies(
     ${verilator}
     V3Lexer_yy_cpp${CMAKE_BUILD_TYPE}