diff --git a/lib/linter/linter.js b/lib/linter/linter.js
index 1d021d1e82e7..c35605b54a2b 100644
--- a/lib/linter/linter.js
+++ b/lib/linter/linter.js
@@ -938,22 +938,25 @@ function runRules(sourceCode, configuredRules, ruleMapper, parserOptions, parser
         });
     });
 
-    const eventGenerator = new CodePathAnalyzer(new NodeEventGenerator(emitter));
+    // only run code path analyzer if the top level node is "Program", skip otherwise
+    if (nodeQueue[0].node.type === "Program") {
+        const eventGenerator = new CodePathAnalyzer(new NodeEventGenerator(emitter));
 
-    nodeQueue.forEach(traversalInfo => {
-        currentNode = traversalInfo.node;
+        nodeQueue.forEach(traversalInfo => {
+            currentNode = traversalInfo.node;
 
-        try {
-            if (traversalInfo.isEntering) {
-                eventGenerator.enterNode(currentNode);
-            } else {
-                eventGenerator.leaveNode(currentNode);
+            try {
+                if (traversalInfo.isEntering) {
+                    eventGenerator.enterNode(currentNode);
+                } else {
+                    eventGenerator.leaveNode(currentNode);
+                }
+            } catch (err) {
+                err.currentNode = currentNode;
+                throw err;
             }
-        } catch (err) {
-            err.currentNode = currentNode;
-            throw err;
-        }
-    });
+        });
+    }
 
     return lintingProblems;
 }
diff --git a/tests/fixtures/parsers/linter-test-parsers.js b/tests/fixtures/parsers/linter-test-parsers.js
index dc81e34ecb9e..9f871a4b5831 100644
--- a/tests/fixtures/parsers/linter-test-parsers.js
+++ b/tests/fixtures/parsers/linter-test-parsers.js
@@ -10,5 +10,6 @@ module.exports = {
     noLineError: require("./no-line-error"),
     enhancedParser2: require("./enhanced-parser2"),
     enhancedParser3: require("./enhanced-parser3"),
-    throwsWithOptions: require("./throws-with-options")
+    throwsWithOptions: require("./throws-with-options"),
+    nonJSParser: require('./non-js-parser')
 };
diff --git a/tests/fixtures/parsers/non-js-parser.js b/tests/fixtures/parsers/non-js-parser.js
new file mode 100644
index 000000000000..86b6d9393673
--- /dev/null
+++ b/tests/fixtures/parsers/non-js-parser.js
@@ -0,0 +1,238 @@
+/**
+ * Source code:
+ * function foo(a: number=0): Foo { }
+ */
+
+exports.parseForESLint = () => ({
+    ast: {
+        "kind": "Document",
+        "definitions": [
+            {
+                "kind": "ObjectTypeExtension",
+                "name": {
+                    "kind": "Name",
+                    "value": "Query",
+                    "loc": {
+                        "start": 12,
+                        "end": 17
+                    },
+                    "type": "Name"
+                },
+                "interfaces": [],
+                "directives": [],
+                "fields": [
+                    {
+                        "kind": "FieldDefinition",
+                        "name": {
+                            "kind": "Name",
+                            "value": "login",
+                            "loc": {
+                                "start": 24,
+                                "end": 29
+                            },
+                            "type": "Name"
+                        },
+                        "arguments": [
+                            {
+                                "kind": "InputValueDefinition",
+                                "name": {
+                                    "kind": "Name",
+                                    "value": "input",
+                                    "loc": {
+                                        "start": 30,
+                                        "end": 35
+                                    },
+                                    "type": "Name"
+                                },
+                                "type": "InputValueDefinition",
+                                "directives": [],
+                                "loc": {
+                                    "start": 30,
+                                    "end": 49
+                                },
+                                "fieldType": {
+                                    "kind": "NonNullType",
+                                    "type": "NonNullType",
+                                    "loc": {
+                                        "start": 37,
+                                        "end": 49
+                                    },
+                                    "fieldType": {
+                                        "kind": "NamedType",
+                                        "name": {
+                                            "kind": "Name",
+                                            "value": "Credentials",
+                                            "loc": {
+                                                "start": 37,
+                                                "end": 48
+                                            },
+                                            "type": "Name"
+                                        },
+                                        "loc": {
+                                            "start": 37,
+                                            "end": 48
+                                        },
+                                        "type": "NamedType"
+                                    }
+                                }
+                            }
+                        ],
+                        "type": "FieldDefinition",
+                        "directives": [],
+                        "loc": {
+                            "start": 24,
+                            "end": 63
+                        },
+                        "fieldType": {
+                            "kind": "NamedType",
+                            "name": {
+                                "kind": "Name",
+                                "value": "UserProfile",
+                                "loc": {
+                                    "start": 52,
+                                    "end": 63
+                                },
+                                "type": "Name"
+                            },
+                            "loc": {
+                                "start": 52,
+                                "end": 63
+                            },
+                            "type": "NamedType"
+                        }
+                    }
+                ],
+                "loc": {
+                    "start": 0,
+                    "end": 65
+                },
+                "type": "ObjectTypeExtension"
+            },
+            {
+                "kind": "InputObjectTypeDefinition",
+                "name": {
+                    "kind": "Name",
+                    "value": "Credentials",
+                    "loc": {
+                        "start": 73,
+                        "end": 84
+                    },
+                    "type": "Name"
+                },
+                "directives": [],
+                "fields": [
+                    {
+                        "kind": "InputValueDefinition",
+                        "name": {
+                            "kind": "Name",
+                            "value": "login",
+                            "loc": {
+                                "start": 91,
+                                "end": 96
+                            },
+                            "type": "Name"
+                        },
+                        "type": "InputValueDefinition",
+                        "directives": [],
+                        "loc": {
+                            "start": 91,
+                            "end": 105
+                        },
+                        "fieldType": {
+                            "kind": "NonNullType",
+                            "type": "NonNullType",
+                            "loc": {
+                                "start": 98,
+                                "end": 105
+                            },
+                            "fieldType": {
+                                "kind": "NamedType",
+                                "name": {
+                                    "kind": "Name",
+                                    "value": "String",
+                                    "loc": {
+                                        "start": 98,
+                                        "end": 104
+                                    },
+                                    "type": "Name"
+                                },
+                                "loc": {
+                                    "start": 98,
+                                    "end": 104
+                                },
+                                "type": "NamedType"
+                            }
+                        }
+                    },
+                    {
+                        "kind": "InputValueDefinition",
+                        "name": {
+                            "kind": "Name",
+                            "value": "password",
+                            "loc": {
+                                "start": 110,
+                                "end": 118
+                            },
+                            "type": "Name"
+                        },
+                        "type": "InputValueDefinition",
+                        "directives": [],
+                        "loc": {
+                            "start": 110,
+                            "end": 127
+                        },
+                        "fieldType": {
+                            "kind": "NonNullType",
+                            "type": "NonNullType",
+                            "loc": {
+                                "start": 120,
+                                "end": 127
+                            },
+                            "fieldType": {
+                                "kind": "NamedType",
+                                "name": {
+                                    "kind": "Name",
+                                    "value": "String",
+                                    "loc": {
+                                        "start": 120,
+                                        "end": 126
+                                    },
+                                    "type": "Name"
+                                },
+                                "loc": {
+                                    "start": 120,
+                                    "end": 126
+                                },
+                                "type": "NamedType"
+                            }
+                        }
+                    }
+                ],
+                "loc": {
+                    "start": 67,
+                    "end": 129
+                },
+                "type": "InputObjectTypeDefinition"
+            }
+        ],
+        "loc": {
+            "start": 0,
+            "end": 130
+        },
+        "type": "Document",
+        "tokens": [],
+        "comments": [],
+        "range": {}
+    },
+    services: {},
+    scopeManager: { variables: [], scopes: [{ set: new Map(), variables: [], through: [] }], getDeclaredVariables: () => {} },
+    visitorKeys: {
+        Document: ['definitions'],
+        ObjectTypeDefinition: ['interfaces', 'directives', 'fields'],
+        ObjectTypeExtension: ['interfaces', 'directives', 'fields'],
+        InputObjectTypeDefinition: ['directives', 'fields'],
+        InputValueDefinition: ['directives', 'fieldType'],
+        FieldDefinition: ['directives', 'fieldType', 'arguments'],
+        EnumTypeDefinition: ['directives', 'values']
+    }
+});
diff --git a/tests/lib/linter/linter.js b/tests/lib/linter/linter.js
index 56d028e5c629..679d045b890d 100644
--- a/tests/lib/linter/linter.js
+++ b/tests/lib/linter/linter.js
@@ -5247,6 +5247,16 @@ var a = "test2";
             assert.strictEqual(messages.length, 0);
         });
 
+        it("should not throw or return errors when the custom parser returns unknown AST nodes", () => {
+            const code = "foo && bar %% baz";
+
+            linter.defineParser("non-js-parser", testParsers.nonJSParser);
+
+            const messages = linter.verify(code, { parser: "non-js-parser" }, filename, true);
+
+            assert.strictEqual(messages.length, 0);
+        });
+
         it("should strip leading line: prefix from parser error", () => {
             linter.defineParser("line-error", testParsers.lineError);
             const messages = linter.verify(";", { parser: "line-error" }, "filename");