diff --git a/libsel4/tools/syscall_stub_gen.py b/libsel4/tools/syscall_stub_gen.py
index 3bc0ba685..f412921b5 100644
--- a/libsel4/tools/syscall_stub_gen.py
+++ b/libsel4/tools/syscall_stub_gen.py
@@ -78,7 +78,7 @@ MAX_MESSAGE_LENGTH = 64
 
 # Headers to include
 INCLUDES = [
-    'autoconf.h', 'sel4/types.h'
+    'sel4/config.h', 'sel4/types.h'
 ]
 
 TYPES = {
diff --git a/tools/bitfield_gen.py b/tools/bitfield_gen.py
index 5efca4689..e1e12372c 100755
--- a/tools/bitfield_gen.py
+++ b/tools/bitfield_gen.py
@@ -56,7 +56,7 @@ def var_name(name, base):
 # Headers to include depending on which environment we are generating code for.
 INCLUDES = {
     'sel4': ['assert.h', 'config.h', 'stdint.h', 'util.h'],
-    'libsel4': ['autoconf.h', 'sel4/simple_types.h', 'sel4/debug_assert.h'],
+    'libsel4': ['sel4/config.h', 'sel4/simple_types.h', 'sel4/debug_assert.h'],
 }
 
 ASSERTS = {
diff --git a/tools/syscall_header_gen.py b/tools/syscall_header_gen.py
index 8ba6e1d00..e6123f8ed 100755
--- a/tools/syscall_header_gen.py
+++ b/tools/syscall_header_gen.py
@@ -96,7 +96,7 @@ LIBSEL4_HEADER_TEMPLATE = """/*
 """ + COMMON_HEADER + """
 #pragma once
 
-#include <autoconf.h>
+#include <sel4/config.h>
 
 typedef enum {
 {%- for condition, list in enum %}