diff --git a/.changeset/fix-custom-claims-override.md b/.changeset/fix-custom-claims-override.md
new file mode 100644
index 000000000..c1158d5d8
--- /dev/null
+++ b/.changeset/fix-custom-claims-override.md
@@ -0,0 +1,10 @@
+---
+"@modelcontextprotocol/client": patch
+---
+
+Fix custom claims not overriding reserved JWT claims in createPrivateKeyJwtAuth
+
+Remove redundant jose setter calls (setIssuer, setSubject, setAudience, setIssuedAt,
+setExpirationTime, setJti) that silently overwrote user-provided custom claims, making
+the runtime behavior match the documented contract that custom claims take precedence
+for overlapping keys.
diff --git a/packages/client/src/client/authExtensions.ts b/packages/client/src/client/authExtensions.ts
index cb476c12f..6148a2ce6 100644
--- a/packages/client/src/client/authExtensions.ts
+++ b/packages/client/src/client/authExtensions.ts
@@ -79,14 +79,13 @@ export function createPrivateKeyJwtAuth(options: {
         }
 
         // Sign JWT
+        // All six reserved claims (iss, sub, aud, iat, exp, jti) are already
+        // present in `claims` via `baseClaims`, and custom overrides from
+        // `options.claims` are merged on top.  We intentionally do NOT call
+        // the jose setter helpers here so the documented "custom claims take
+        // precedence" contract is honored.
         const assertion = await new jose.SignJWT(claims)
             .setProtectedHeader({ alg, typ: 'JWT' })
-            .setIssuer(options.issuer)
-            .setSubject(options.subject)
-            .setAudience(audience)
-            .setIssuedAt(now)
-            .setExpirationTime(now + lifetimeSeconds)
-            .setJti(jti)
             .sign(key as unknown as Uint8Array | CryptoKey);
 
         params.set('client_assertion', assertion);
diff --git a/packages/client/test/client/authExtensions.test.ts b/packages/client/test/client/authExtensions.test.ts
index 16c3ea33e..9e6eb9b62 100644
--- a/packages/client/test/client/authExtensions.test.ts
+++ b/packages/client/test/client/authExtensions.test.ts
@@ -448,6 +448,35 @@ describe('createPrivateKeyJwtAuth', () => {
         expect(decoded.sub).toBe('client-id');
     });
 
+    it('allows custom claims to override reserved JWT claims', async () => {
+        const addClientAuth = createPrivateKeyJwtAuth({
+            issuer: 'client-id',
+            subject: 'client-id',
+            privateKey: 'a-string-secret-at-least-256-bits-long',
+            alg: 'HS256',
+            audience: 'https://aud.example.com',
+            claims: {
+                iss: 'override-issuer',
+                sub: 'override-subject',
+                aud: 'https://override.example.com',
+                tenant_id: 'org-123'
+            }
+        });
+
+        const params = new URLSearchParams();
+        await addClientAuth(new Headers(), params, 'https://auth.example.com/token', undefined);
+
+        const assertion = params.get('client_assertion');
+        expect(assertion).toBeTruthy();
+
+        const jose = await import('jose');
+        const decoded = jose.decodeJwt(assertion!);
+        expect(decoded.iss).toBe('override-issuer');
+        expect(decoded.sub).toBe('override-subject');
+        expect(decoded.aud).toBe('https://override.example.com');
+        expect(decoded.tenant_id).toBe('org-123');
+    });
+
     it('passes custom claims through PrivateKeyJwtProvider', async () => {
         const provider = new PrivateKeyJwtProvider({
             clientId: 'client-id',