diff --git a/plugin/builtin/patchtransformer/PatchTransformer.go b/plugin/builtin/patchtransformer/PatchTransformer.go
index 04f15b7ee0..062e57930a 100644
--- a/plugin/builtin/patchtransformer/PatchTransformer.go
+++ b/plugin/builtin/patchtransformer/PatchTransformer.go
@@ -59,8 +59,9 @@ func (p *plugin) Config(h *resmap.PluginHelpers, c []byte) error {
 	patchesSM, errSM := h.ResmapFactory().RF().SliceFromBytes([]byte(p.patchText))
 	patchesJson, errJson := jsonPatchFromBytes([]byte(p.patchText))
 
-	if (errSM == nil && errJson == nil) ||
-		(patchesSM != nil && patchesJson != nil) {
+	if ((errSM == nil && errJson == nil) ||
+		(patchesSM != nil && patchesJson != nil)) &&
+		(len(patchesSM) > 0 && len(patchesJson) > 0) {
 		return fmt.Errorf(
 			"illegally qualifies as both an SM and JSON patch: %s",
 			p.patchSource)
diff --git a/plugin/builtin/patchtransformer/PatchTransformer_test.go b/plugin/builtin/patchtransformer/PatchTransformer_test.go
index 805e5f99e4..24bfb0040a 100644
--- a/plugin/builtin/patchtransformer/PatchTransformer_test.go
+++ b/plugin/builtin/patchtransformer/PatchTransformer_test.go
@@ -1108,3 +1108,32 @@ spec:
         name: test-deployment
 `)
 }
+
+func TestPatchTransformerPatchEmpty(t *testing.T) {
+	th := kusttest_test.MakeEnhancedHarness(t).
+		PrepBuiltin("PatchTransformer")
+	defer th.Reset()
+
+	th.RunTransformerAndCheckError(`
+`, someDeploymentResources, func(t *testing.T, err error) {
+		if err != nil {
+			t.Fatalf("unexpected error")
+		}
+	})
+}
+
+func TestPatchTransformerPatchEmptyOnlyComments(t *testing.T) {
+	th := kusttest_test.MakeEnhancedHarness(t).
+		PrepBuiltin("PatchTransformer")
+	defer th.Reset()
+
+	th.RunTransformerAndCheckError(`
+# File with only comments
+
+# Is a virtually empty yaml
+`, someDeploymentResources, func(t *testing.T, err error) {
+		if err != nil {
+			t.Fatalf("unexpected error")
+		}
+	})
+}