diff --git a/src/compiler/checker.ts b/src/compiler/checker.ts
index c6df5749e4a..78fd663bbb9 100644
--- a/src/compiler/checker.ts
+++ b/src/compiler/checker.ts
@@ -18104,7 +18104,8 @@ namespace ts {
                     return true;
                 }
             }
-            else {
+            else if (!((source.flags | target.flags) & (TypeFlags.UnionOrIntersection | TypeFlags.IndexedAccess | TypeFlags.Conditional | TypeFlags.Substitution))) {
+                // We have excluded types that may simplify to other forms, so types must have identical flags
                 if (source.flags !== target.flags) return false;
                 if (source.flags & TypeFlags.Singleton) return true;
             }
diff --git a/tests/baselines/reference/identityRelationNeverTypes.js b/tests/baselines/reference/identityRelationNeverTypes.js
new file mode 100644
index 00000000000..efe85defc1b
--- /dev/null
+++ b/tests/baselines/reference/identityRelationNeverTypes.js
@@ -0,0 +1,42 @@
+//// [identityRelationNeverTypes.ts]
+// Repro from #47996
+
+type Equals<A, B> = (<T>() => T extends B ? 1 : 0) extends (<T>() => T extends A ? 1 : 0) ? true : false;
+
+declare class State<TContext> {
+    _context: TContext;
+    _value: string;
+    matches<TSV extends string>(stateValue: TSV): this is State<TContext> & { value: TSV };
+}
+
+function f1(state: State<{ foo: number }>) {
+    if (state.matches('a') && state.matches('a.b')) {
+        state;  // never
+        type T1 = Equals<typeof state, never>;  // true
+        type T2 = Equals<never, never>;  // true
+    }
+}
+
+
+//// [identityRelationNeverTypes.js]
+"use strict";
+// Repro from #47996
+function f1(state) {
+    if (state.matches('a') && state.matches('a.b')) {
+        state; // never
+    }
+}
+
+
+//// [identityRelationNeverTypes.d.ts]
+declare type Equals<A, B> = (<T>() => T extends B ? 1 : 0) extends (<T>() => T extends A ? 1 : 0) ? true : false;
+declare class State<TContext> {
+    _context: TContext;
+    _value: string;
+    matches<TSV extends string>(stateValue: TSV): this is State<TContext> & {
+        value: TSV;
+    };
+}
+declare function f1(state: State<{
+    foo: number;
+}>): void;
diff --git a/tests/baselines/reference/identityRelationNeverTypes.symbols b/tests/baselines/reference/identityRelationNeverTypes.symbols
new file mode 100644
index 00000000000..0bc98f71dca
--- /dev/null
+++ b/tests/baselines/reference/identityRelationNeverTypes.symbols
@@ -0,0 +1,64 @@
+=== tests/cases/compiler/identityRelationNeverTypes.ts ===
+// Repro from #47996
+
+type Equals<A, B> = (<T>() => T extends B ? 1 : 0) extends (<T>() => T extends A ? 1 : 0) ? true : false;
+>Equals : Symbol(Equals, Decl(identityRelationNeverTypes.ts, 0, 0))
+>A : Symbol(A, Decl(identityRelationNeverTypes.ts, 2, 12))
+>B : Symbol(B, Decl(identityRelationNeverTypes.ts, 2, 14))
+>T : Symbol(T, Decl(identityRelationNeverTypes.ts, 2, 22))
+>T : Symbol(T, Decl(identityRelationNeverTypes.ts, 2, 22))
+>B : Symbol(B, Decl(identityRelationNeverTypes.ts, 2, 14))
+>T : Symbol(T, Decl(identityRelationNeverTypes.ts, 2, 61))
+>T : Symbol(T, Decl(identityRelationNeverTypes.ts, 2, 61))
+>A : Symbol(A, Decl(identityRelationNeverTypes.ts, 2, 12))
+
+declare class State<TContext> {
+>State : Symbol(State, Decl(identityRelationNeverTypes.ts, 2, 105))
+>TContext : Symbol(TContext, Decl(identityRelationNeverTypes.ts, 4, 20))
+
+    _context: TContext;
+>_context : Symbol(State._context, Decl(identityRelationNeverTypes.ts, 4, 31))
+>TContext : Symbol(TContext, Decl(identityRelationNeverTypes.ts, 4, 20))
+
+    _value: string;
+>_value : Symbol(State._value, Decl(identityRelationNeverTypes.ts, 5, 23))
+
+    matches<TSV extends string>(stateValue: TSV): this is State<TContext> & { value: TSV };
+>matches : Symbol(State.matches, Decl(identityRelationNeverTypes.ts, 6, 19))
+>TSV : Symbol(TSV, Decl(identityRelationNeverTypes.ts, 7, 12))
+>stateValue : Symbol(stateValue, Decl(identityRelationNeverTypes.ts, 7, 32))
+>TSV : Symbol(TSV, Decl(identityRelationNeverTypes.ts, 7, 12))
+>State : Symbol(State, Decl(identityRelationNeverTypes.ts, 2, 105))
+>TContext : Symbol(TContext, Decl(identityRelationNeverTypes.ts, 4, 20))
+>value : Symbol(value, Decl(identityRelationNeverTypes.ts, 7, 77))
+>TSV : Symbol(TSV, Decl(identityRelationNeverTypes.ts, 7, 12))
+}
+
+function f1(state: State<{ foo: number }>) {
+>f1 : Symbol(f1, Decl(identityRelationNeverTypes.ts, 8, 1))
+>state : Symbol(state, Decl(identityRelationNeverTypes.ts, 10, 12))
+>State : Symbol(State, Decl(identityRelationNeverTypes.ts, 2, 105))
+>foo : Symbol(foo, Decl(identityRelationNeverTypes.ts, 10, 26))
+
+    if (state.matches('a') && state.matches('a.b')) {
+>state.matches : Symbol(State.matches, Decl(identityRelationNeverTypes.ts, 6, 19))
+>state : Symbol(state, Decl(identityRelationNeverTypes.ts, 10, 12))
+>matches : Symbol(State.matches, Decl(identityRelationNeverTypes.ts, 6, 19))
+>state.matches : Symbol(State.matches, Decl(identityRelationNeverTypes.ts, 6, 19))
+>state : Symbol(state, Decl(identityRelationNeverTypes.ts, 10, 12))
+>matches : Symbol(State.matches, Decl(identityRelationNeverTypes.ts, 6, 19))
+
+        state;  // never
+>state : Symbol(state, Decl(identityRelationNeverTypes.ts, 10, 12))
+
+        type T1 = Equals<typeof state, never>;  // true
+>T1 : Symbol(T1, Decl(identityRelationNeverTypes.ts, 12, 14))
+>Equals : Symbol(Equals, Decl(identityRelationNeverTypes.ts, 0, 0))
+>state : Symbol(state, Decl(identityRelationNeverTypes.ts, 10, 12))
+
+        type T2 = Equals<never, never>;  // true
+>T2 : Symbol(T2, Decl(identityRelationNeverTypes.ts, 13, 46))
+>Equals : Symbol(Equals, Decl(identityRelationNeverTypes.ts, 0, 0))
+    }
+}
+
diff --git a/tests/baselines/reference/identityRelationNeverTypes.types b/tests/baselines/reference/identityRelationNeverTypes.types
new file mode 100644
index 00000000000..d94a3794c78
--- /dev/null
+++ b/tests/baselines/reference/identityRelationNeverTypes.types
@@ -0,0 +1,53 @@
+=== tests/cases/compiler/identityRelationNeverTypes.ts ===
+// Repro from #47996
+
+type Equals<A, B> = (<T>() => T extends B ? 1 : 0) extends (<T>() => T extends A ? 1 : 0) ? true : false;
+>Equals : Equals<A, B>
+>true : true
+>false : false
+
+declare class State<TContext> {
+>State : State<TContext>
+
+    _context: TContext;
+>_context : TContext
+
+    _value: string;
+>_value : string
+
+    matches<TSV extends string>(stateValue: TSV): this is State<TContext> & { value: TSV };
+>matches : <TSV extends string>(stateValue: TSV) => this is State<TContext> & { value: TSV; }
+>stateValue : TSV
+>value : TSV
+}
+
+function f1(state: State<{ foo: number }>) {
+>f1 : (state: State<{    foo: number;}>) => void
+>state : State<{ foo: number; }>
+>foo : number
+
+    if (state.matches('a') && state.matches('a.b')) {
+>state.matches('a') && state.matches('a.b') : boolean
+>state.matches('a') : boolean
+>state.matches : <TSV extends string>(stateValue: TSV) => this is State<{ foo: number; }> & { value: TSV; }
+>state : State<{ foo: number; }>
+>matches : <TSV extends string>(stateValue: TSV) => this is State<{ foo: number; }> & { value: TSV; }
+>'a' : "a"
+>state.matches('a.b') : boolean
+>state.matches : <TSV extends string>(stateValue: TSV) => this is State<{ foo: number; }> & { value: TSV; }
+>state : State<{ foo: number; }> & { value: "a"; }
+>matches : <TSV extends string>(stateValue: TSV) => this is State<{ foo: number; }> & { value: TSV; }
+>'a.b' : "a.b"
+
+        state;  // never
+>state : never
+
+        type T1 = Equals<typeof state, never>;  // true
+>T1 : true
+>state : never
+
+        type T2 = Equals<never, never>;  // true
+>T2 : true
+    }
+}
+
diff --git a/tests/cases/compiler/identityRelationNeverTypes.ts b/tests/cases/compiler/identityRelationNeverTypes.ts
new file mode 100644
index 00000000000..62d233bcf06
--- /dev/null
+++ b/tests/cases/compiler/identityRelationNeverTypes.ts
@@ -0,0 +1,20 @@
+// @strict: true
+// @declaration: true
+
+// Repro from #47996
+
+type Equals<A, B> = (<T>() => T extends B ? 1 : 0) extends (<T>() => T extends A ? 1 : 0) ? true : false;
+
+declare class State<TContext> {
+    _context: TContext;
+    _value: string;
+    matches<TSV extends string>(stateValue: TSV): this is State<TContext> & { value: TSV };
+}
+
+function f1(state: State<{ foo: number }>) {
+    if (state.matches('a') && state.matches('a.b')) {
+        state;  // never
+        type T1 = Equals<typeof state, never>;  // true
+        type T2 = Equals<never, never>;  // true
+    }
+}