diff --git a/check/check-special-flags b/check/check-special-flags
index 136160a..c0a9ebb 100755
--- a/check/check-special-flags
+++ b/check/check-special-flags
@@ -4,7 +4,7 @@ set -e
 
 . ${srcdir}/common
 
-RESULT="-idirafter /after1 -idirafter /after2 -I/foo -I/bar"
+RESULT="-isystem /system1 -idirafter /after1 -idirafter /after2 -isystem /system2 -I/foo -I/bar"
 run_test --cflags special-flags
 
 RESULT="-framework Foo -lsimple -framework Bar"
diff --git a/check/special-flags.pc b/check/special-flags.pc
index 269fd36..318eab0 100644
--- a/check/special-flags.pc
+++ b/check/special-flags.pc
@@ -8,4 +8,4 @@ Description: Dummy pkgconfig test package for testing pkgconfig
 Version: 1.0.0
 Requires:
 Libs: -framework Foo -lsimple -framework Bar
-Cflags: -I/foo -idirafter /after1 -I/bar -idirafter /after2
+Cflags: -I/foo -isystem /system1 -idirafter /after1 -I/bar -idirafter /after2 -isystem /system2
diff --git a/parse.c b/parse.c
index 87e5191..60785ea 100644
--- a/parse.c
+++ b/parse.c
@@ -851,17 +851,19 @@ parse_cflags (Package *pkg, const char *str, const char *path)
           flag->arg = g_strconcat ("-I", p, NULL);
           pkg->cflags = g_list_prepend (pkg->cflags, flag);
         }
-      else if (strcmp("-idirafter", arg) == 0 && i+1 < argc)
+      else if ((strcmp ("-idirafter", arg) == 0 ||
+                strcmp ("-isystem", arg) == 0) &&
+               i+1 < argc)
         {
-          char *dirafter, *tmp;
+          char *option, *tmp;
 
           tmp = trim_string (argv[i+1]);
-          dirafter = strdup_escape_shell (tmp);
+          option = strdup_escape_shell (tmp);
           flag->type = CFLAGS_OTHER;
-          flag->arg = g_strconcat (arg, " ", dirafter, NULL);
+          flag->arg = g_strconcat (arg, " ", option, NULL);
           pkg->cflags = g_list_prepend (pkg->cflags, flag);
           i++;
-          g_free (dirafter);
+          g_free (option);
           g_free (tmp);
         }
       else if (*arg != '\0')