diff --git a/cgo/cgo.go b/cgo/cgo.go
index efaa949c..15b38869 100644
--- a/cgo/cgo.go
+++ b/cgo/cgo.go
@@ -197,7 +197,7 @@ func GoBytes(ptr unsafe.Pointer, length C.int) []byte {
 // functions), the CFLAGS and LDFLAGS found in #cgo lines, and a map of file
 // hashes of the accessed C header files. If there is one or more error, it
 // returns these in the []error slice but still modifies the AST.
-func Process(files []*ast.File, dir string, fset *token.FileSet, cflags []string) (*ast.File, []string, []string, []string, map[string][]byte, []error) {
+func Process(files []*ast.File, dir string, fset *token.FileSet, cflags []string, clangHeaders string) (*ast.File, []string, []string, []string, map[string][]byte, []error) {
 	p := &cgoPackage{
 		currentDir:      dir,
 		fset:            fset,
@@ -333,6 +333,9 @@ func Process(files []*ast.File, dir string, fset *token.FileSet, cflags []string
 	// have better alternatives anyway.
 	cflagsForCGo := append([]string{"-D_FORTIFY_SOURCE=0"}, cflags...)
 	cflagsForCGo = append(cflagsForCGo, p.cflags...)
+	if clangHeaders != "" {
+		cflagsForCGo = append(cflagsForCGo, "-isystem", clangHeaders)
+	}
 
 	// Process CGo imports for each file.
 	for i, f := range files {
diff --git a/cgo/cgo_test.go b/cgo/cgo_test.go
index b46c36dd..cbb0f589 100644
--- a/cgo/cgo_test.go
+++ b/cgo/cgo_test.go
@@ -63,7 +63,7 @@ func TestCGo(t *testing.T) {
 			}
 
 			// Process the AST with CGo.
-			cgoAST, _, _, _, _, cgoErrors := Process([]*ast.File{f}, "testdata", fset, cflags)
+			cgoAST, _, _, _, _, cgoErrors := Process([]*ast.File{f}, "testdata", fset, cflags, "")
 
 			// Check the AST for type errors.
 			var typecheckErrors []error
diff --git a/loader/loader.go b/loader/loader.go
index b8db2587..e9de2ec2 100644
--- a/loader/loader.go
+++ b/loader/loader.go
@@ -418,10 +418,7 @@ func (p *Package) parseFiles() ([]*ast.File, error) {
 		var initialCFlags []string
 		initialCFlags = append(initialCFlags, p.program.config.CFlags()...)
 		initialCFlags = append(initialCFlags, "-I"+p.Dir)
-		if p.program.clangHeaders != "" {
-			initialCFlags = append(initialCFlags, "-isystem", p.program.clangHeaders)
-		}
-		generated, headerCode, cflags, ldflags, accessedFiles, errs := cgo.Process(files, p.program.workingDir, p.program.fset, initialCFlags)
+		generated, headerCode, cflags, ldflags, accessedFiles, errs := cgo.Process(files, p.program.workingDir, p.program.fset, initialCFlags, p.program.clangHeaders)
 		p.CFlags = append(initialCFlags, cflags...)
 		p.CGoHeaders = headerCode
 		for path, hash := range accessedFiles {