diff --git a/src/compiler/checker.ts b/src/compiler/checker.ts
index 21518ca34d5..2f020f46f22 100644
--- a/src/compiler/checker.ts
+++ b/src/compiler/checker.ts
@@ -10616,9 +10616,9 @@ namespace ts {
         function isTypeDerivedFrom(source: Type, target: Type): boolean {
             return source.flags & TypeFlags.Union ? every((<UnionType>source).types, t => isTypeDerivedFrom(t, target)) :
                 target.flags & TypeFlags.Union ? some((<UnionType>target).types, t => isTypeDerivedFrom(source, t)) :
-                source.flags & TypeFlags.Primitive && !(target.flags & TypeFlags.Primitive) ? false :
                 source.flags & TypeFlags.InstantiableNonPrimitive ? isTypeDerivedFrom(getBaseConstraintOfType(source) || emptyObjectType, target) :
-                target === globalObjectType || target === globalFunctionType ? isTypeSubtypeOf(source, target) :
+                target === globalObjectType ? !!(source.flags & (TypeFlags.Object | TypeFlags.NonPrimitive)) :
+                target === globalFunctionType ? isFunctionObjectType(source as ObjectType) :
                 hasBaseType(source, getTargetType(target));
             }
 
@@ -15371,7 +15371,7 @@ namespace ts {
 
                 // Check that right operand is a function type with a prototype property
                 const rightType = getTypeOfExpression(expr.right);
-                if (!isTypeSubtypeOf(rightType, globalFunctionType)) {
+                if (!isTypeDerivedFrom(rightType, globalFunctionType)) {
                     return type;
                 }
 
diff --git a/tests/baselines/reference/controlFlowInstanceofExtendsFunction.js b/tests/baselines/reference/controlFlowInstanceofExtendsFunction.js
new file mode 100644
index 00000000000..950aa25b576
--- /dev/null
+++ b/tests/baselines/reference/controlFlowInstanceofExtendsFunction.js
@@ -0,0 +1,61 @@
+//// [controlFlowInstanceofExtendsFunction.ts]
+declare global {
+    interface Function {
+        now(): string;
+    }
+}
+
+Function.prototype.now = function () {
+    return "now"
+}
+
+class X {
+    static now() {
+        return {}
+    }
+
+    why() {
+
+    }
+}
+
+class Y {
+
+}
+
+console.log(X.now()) // works as expected
+console.log(Y.now()) // works as expected
+
+export const x: X | number = Math.random() > 0.5 ? new X() : 1
+
+if (x instanceof X) {
+    x.why() // should compile
+}
+
+//// [controlFlowInstanceofExtendsFunction.js]
+"use strict";
+exports.__esModule = true;
+Function.prototype.now = function () {
+    return "now";
+};
+var X = /** @class */ (function () {
+    function X() {
+    }
+    X.now = function () {
+        return {};
+    };
+    X.prototype.why = function () {
+    };
+    return X;
+}());
+var Y = /** @class */ (function () {
+    function Y() {
+    }
+    return Y;
+}());
+console.log(X.now()); // works as expected
+console.log(Y.now()); // works as expected
+exports.x = Math.random() > 0.5 ? new X() : 1;
+if (exports.x instanceof X) {
+    exports.x.why(); // should compile
+}
diff --git a/tests/baselines/reference/controlFlowInstanceofExtendsFunction.symbols b/tests/baselines/reference/controlFlowInstanceofExtendsFunction.symbols
new file mode 100644
index 00000000000..c5ac2e71eda
--- /dev/null
+++ b/tests/baselines/reference/controlFlowInstanceofExtendsFunction.symbols
@@ -0,0 +1,75 @@
+=== tests/cases/conformance/controlFlow/controlFlowInstanceofExtendsFunction.ts ===
+declare global {
+>global : Symbol(global, Decl(controlFlowInstanceofExtendsFunction.ts, 0, 0))
+
+    interface Function {
+>Function : Symbol(Function, Decl(lib.es5.d.ts, --, --), Decl(lib.es5.d.ts, --, --), Decl(controlFlowInstanceofExtendsFunction.ts, 0, 16))
+
+        now(): string;
+>now : Symbol(Function.now, Decl(controlFlowInstanceofExtendsFunction.ts, 1, 24))
+    }
+}
+
+Function.prototype.now = function () {
+>Function.prototype.now : Symbol(Function.now, Decl(controlFlowInstanceofExtendsFunction.ts, 1, 24))
+>Function.prototype : Symbol(FunctionConstructor.prototype, Decl(lib.es5.d.ts, --, --))
+>Function : Symbol(Function, Decl(lib.es5.d.ts, --, --), Decl(lib.es5.d.ts, --, --), Decl(controlFlowInstanceofExtendsFunction.ts, 0, 16))
+>prototype : Symbol(FunctionConstructor.prototype, Decl(lib.es5.d.ts, --, --))
+>now : Symbol(Function.now, Decl(controlFlowInstanceofExtendsFunction.ts, 1, 24))
+
+    return "now"
+}
+
+class X {
+>X : Symbol(X, Decl(controlFlowInstanceofExtendsFunction.ts, 8, 1))
+
+    static now() {
+>now : Symbol(X.now, Decl(controlFlowInstanceofExtendsFunction.ts, 10, 9))
+
+        return {}
+    }
+
+    why() {
+>why : Symbol(X.why, Decl(controlFlowInstanceofExtendsFunction.ts, 13, 5))
+
+    }
+}
+
+class Y {
+>Y : Symbol(Y, Decl(controlFlowInstanceofExtendsFunction.ts, 18, 1))
+
+}
+
+console.log(X.now()) // works as expected
+>console.log : Symbol(Console.log, Decl(lib.dom.d.ts, --, --))
+>console : Symbol(console, Decl(lib.dom.d.ts, --, --))
+>log : Symbol(Console.log, Decl(lib.dom.d.ts, --, --))
+>X.now : Symbol(X.now, Decl(controlFlowInstanceofExtendsFunction.ts, 10, 9))
+>X : Symbol(X, Decl(controlFlowInstanceofExtendsFunction.ts, 8, 1))
+>now : Symbol(X.now, Decl(controlFlowInstanceofExtendsFunction.ts, 10, 9))
+
+console.log(Y.now()) // works as expected
+>console.log : Symbol(Console.log, Decl(lib.dom.d.ts, --, --))
+>console : Symbol(console, Decl(lib.dom.d.ts, --, --))
+>log : Symbol(Console.log, Decl(lib.dom.d.ts, --, --))
+>Y.now : Symbol(Function.now, Decl(controlFlowInstanceofExtendsFunction.ts, 1, 24))
+>Y : Symbol(Y, Decl(controlFlowInstanceofExtendsFunction.ts, 18, 1))
+>now : Symbol(Function.now, Decl(controlFlowInstanceofExtendsFunction.ts, 1, 24))
+
+export const x: X | number = Math.random() > 0.5 ? new X() : 1
+>x : Symbol(x, Decl(controlFlowInstanceofExtendsFunction.ts, 27, 12))
+>X : Symbol(X, Decl(controlFlowInstanceofExtendsFunction.ts, 8, 1))
+>Math.random : Symbol(Math.random, Decl(lib.es5.d.ts, --, --))
+>Math : Symbol(Math, Decl(lib.es5.d.ts, --, --), Decl(lib.es5.d.ts, --, --))
+>random : Symbol(Math.random, Decl(lib.es5.d.ts, --, --))
+>X : Symbol(X, Decl(controlFlowInstanceofExtendsFunction.ts, 8, 1))
+
+if (x instanceof X) {
+>x : Symbol(x, Decl(controlFlowInstanceofExtendsFunction.ts, 27, 12))
+>X : Symbol(X, Decl(controlFlowInstanceofExtendsFunction.ts, 8, 1))
+
+    x.why() // should compile
+>x.why : Symbol(X.why, Decl(controlFlowInstanceofExtendsFunction.ts, 13, 5))
+>x : Symbol(x, Decl(controlFlowInstanceofExtendsFunction.ts, 27, 12))
+>why : Symbol(X.why, Decl(controlFlowInstanceofExtendsFunction.ts, 13, 5))
+}
diff --git a/tests/baselines/reference/controlFlowInstanceofExtendsFunction.types b/tests/baselines/reference/controlFlowInstanceofExtendsFunction.types
new file mode 100644
index 00000000000..397b0e2e76a
--- /dev/null
+++ b/tests/baselines/reference/controlFlowInstanceofExtendsFunction.types
@@ -0,0 +1,88 @@
+=== tests/cases/conformance/controlFlow/controlFlowInstanceofExtendsFunction.ts ===
+declare global {
+>global : any
+
+    interface Function {
+        now(): string;
+>now : () => string
+    }
+}
+
+Function.prototype.now = function () {
+>Function.prototype.now = function () {    return "now"} : () => string
+>Function.prototype.now : () => string
+>Function.prototype : Function
+>Function : FunctionConstructor
+>prototype : Function
+>now : () => string
+>function () {    return "now"} : () => string
+
+    return "now"
+>"now" : "now"
+}
+
+class X {
+>X : X
+
+    static now() {
+>now : () => {}
+
+        return {}
+>{} : {}
+    }
+
+    why() {
+>why : () => void
+
+    }
+}
+
+class Y {
+>Y : Y
+
+}
+
+console.log(X.now()) // works as expected
+>console.log(X.now()) : void
+>console.log : (message?: any, ...optionalParams: any[]) => void
+>console : Console
+>log : (message?: any, ...optionalParams: any[]) => void
+>X.now() : {}
+>X.now : () => {}
+>X : typeof X
+>now : () => {}
+
+console.log(Y.now()) // works as expected
+>console.log(Y.now()) : void
+>console.log : (message?: any, ...optionalParams: any[]) => void
+>console : Console
+>log : (message?: any, ...optionalParams: any[]) => void
+>Y.now() : string
+>Y.now : () => string
+>Y : typeof Y
+>now : () => string
+
+export const x: X | number = Math.random() > 0.5 ? new X() : 1
+>x : number | X
+>Math.random() > 0.5 ? new X() : 1 : X | 1
+>Math.random() > 0.5 : boolean
+>Math.random() : number
+>Math.random : () => number
+>Math : Math
+>random : () => number
+>0.5 : 0.5
+>new X() : X
+>X : typeof X
+>1 : 1
+
+if (x instanceof X) {
+>x instanceof X : boolean
+>x : number | X
+>X : typeof X
+
+    x.why() // should compile
+>x.why() : void
+>x.why : () => void
+>x : X
+>why : () => void
+}
diff --git a/tests/cases/conformance/controlFlow/controlFlowInstanceofExtendsFunction.ts b/tests/cases/conformance/controlFlow/controlFlowInstanceofExtendsFunction.ts
new file mode 100644
index 00000000000..4a1ff7ff867
--- /dev/null
+++ b/tests/cases/conformance/controlFlow/controlFlowInstanceofExtendsFunction.ts
@@ -0,0 +1,32 @@
+declare global {
+    interface Function {
+        now(): string;
+    }
+}
+
+Function.prototype.now = function () {
+    return "now"
+}
+
+class X {
+    static now() {
+        return {}
+    }
+
+    why() {
+
+    }
+}
+
+class Y {
+
+}
+
+console.log(X.now()) // works as expected
+console.log(Y.now()) // works as expected
+
+export const x: X | number = Math.random() > 0.5 ? new X() : 1
+
+if (x instanceof X) {
+    x.why() // should compile
+}
\ No newline at end of file