diff --git a/api/internal/builtins/PatchTransformer.go b/api/internal/builtins/PatchTransformer.go
index 8e6eb41128..05d96f23ca 100644
--- a/api/internal/builtins/PatchTransformer.go
+++ b/api/internal/builtins/PatchTransformer.go
@@ -56,8 +56,9 @@ func (p *PatchTransformerPlugin) 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.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..5535b6690a 100644
--- a/plugin/builtin/patchtransformer/PatchTransformer_test.go
+++ b/plugin/builtin/patchtransformer/PatchTransformer_test.go
@@ -1108,3 +1108,54 @@ spec:
         name: test-deployment
 `)
 }
+
+func TestPatchTransformerPatchEmpty(t *testing.T) {
+	th := kusttest_test.MakeEnhancedHarness(t).
+		PrepBuiltin("PatchTransformer")
+	defer th.Reset()
+
+	th.WriteF("patch.yaml", `
+  `)
+
+	th.RunTransformerAndCheckError(`
+apiVersion: builtin
+kind: PatchTransformer
+metadata:
+  name: notImportantHere
+path: patch.yaml
+target:
+  name: myDeploy
+`, someDeploymentResources, func(t *testing.T, err error) {
+		t.Helper()
+		if err != nil {
+			t.Fatalf("unexpected error")
+		}
+	})
+}
+
+func TestPatchTransformerPatchEmptyOnlyComments(t *testing.T) {
+	th := kusttest_test.MakeEnhancedHarness(t).
+		PrepBuiltin("PatchTransformer")
+	defer th.Reset()
+
+	th.WriteF("patch.yaml", `
+# File with only comments
+
+# Is a virtually empty yaml
+`)
+
+	th.RunTransformerAndCheckError(`
+apiVersion: builtin
+kind: PatchTransformer
+metadata:
+  name: notImportantHere
+path: patch.yaml
+target:
+  name: myDeploy
+`, someDeploymentResources, func(t *testing.T, err error) {
+		t.Helper()
+		if err != nil {
+			t.Fatalf("unexpected error")
+		}
+	})
+}