diff --git a/.changeset/fair-bobcats-pull.md b/.changeset/fair-bobcats-pull.md
new file mode 100644
index 0000000000..aa766d6104
--- /dev/null
+++ b/.changeset/fair-bobcats-pull.md
@@ -0,0 +1,8 @@
+---
+'@clerk/backend': patch
+'@clerk/types': patch
+---
+
+Add type-level validation to prevent server-side usage of system permissions
+
+System permissions (e.g., `org:sys_domains:manage`) are intentionally excluded from session claims to maintain reasonable JWT sizes. For more information, refer to our docs: https://clerk.com/docs/organizations/roles-permissions#system-permissions
diff --git a/packages/backend/src/tokens/authObjects.ts b/packages/backend/src/tokens/authObjects.ts
index e24df5830c..a0b967cb4d 100644
--- a/packages/backend/src/tokens/authObjects.ts
+++ b/packages/backend/src/tokens/authObjects.ts
@@ -1,7 +1,7 @@
 import { createCheckAuthorization } from '@clerk/shared/authorization';
 import type {
   ActClaim,
-  CheckAuthorizationWithCustomPermissions,
+  CheckAuthorizationFromSessionClaims,
   JwtPayload,
   OrganizationCustomPermissionKey,
   OrganizationCustomRoleKey,
@@ -42,7 +42,7 @@ export type SignedInAuthObject = {
    */
   factorVerificationAge: [number, number] | null;
   getToken: ServerGetToken;
-  has: CheckAuthorizationWithCustomPermissions;
+  has: CheckAuthorizationFromSessionClaims;
   debug: AuthObjectDebug;
 };
 
@@ -65,7 +65,7 @@ export type SignedOutAuthObject = {
    */
   factorVerificationAge: null;
   getToken: ServerGetToken;
-  has: CheckAuthorizationWithCustomPermissions;
+  has: CheckAuthorizationFromSessionClaims;
   debug: AuthObjectDebug;
 };
 
diff --git a/packages/nextjs/src/server/__tests__/clerkMiddleware.test.ts b/packages/nextjs/src/server/__tests__/clerkMiddleware.test.ts
index 9d06d9e10a..5d2429fb16 100644
--- a/packages/nextjs/src/server/__tests__/clerkMiddleware.test.ts
+++ b/packages/nextjs/src/server/__tests__/clerkMiddleware.test.ts
@@ -113,6 +113,13 @@ describe('ClerkMiddleware type tests', () => {
     clerkMiddlewareMock();
   });
 
+  it('prevents usage of system permissions with auth.has()', () => {
+    clerkMiddlewareMock(async (auth, _event, _request) => {
+      // @ts-expect-error - system permissions are not allowed
+      (await auth()).has({ permission: 'org:sys_foo' });
+    });
+  });
+
   describe('Multi domain', () => {
     const defaultProps = { publishableKey: '', secretKey: '' };
 
diff --git a/packages/types/src/jwtv2.ts b/packages/types/src/jwtv2.ts
index 73ef4232f4..3bd27594f9 100644
--- a/packages/types/src/jwtv2.ts
+++ b/packages/types/src/jwtv2.ts
@@ -97,7 +97,7 @@ export interface JwtPayload extends CustomJwtSessionClaims {
   org_role?: OrganizationCustomRoleKey;
 
   /**
-   * Active organization role
+   * Active organization permissions
    */
   org_permissions?: OrganizationCustomPermissionKey[];
 
diff --git a/packages/types/src/organizationMembership.ts b/packages/types/src/organizationMembership.ts
index 8a010d1991..93cf0be204 100644
--- a/packages/types/src/organizationMembership.ts
+++ b/packages/types/src/organizationMembership.ts
@@ -68,13 +68,14 @@ export type OrganizationCustomRoleKey = ClerkAuthorization extends Placeholder
     : Base['role']
   : Base['role'];
 
+export type OrganizationSystemPermissionPrefix = 'org:sys_';
 export type OrganizationSystemPermissionKey =
-  | 'org:sys_domains:manage'
-  | 'org:sys_profile:manage'
-  | 'org:sys_profile:delete'
-  | 'org:sys_memberships:read'
-  | 'org:sys_memberships:manage'
-  | 'org:sys_domains:read';
+  | `${OrganizationSystemPermissionPrefix}domains:manage`
+  | `${OrganizationSystemPermissionPrefix}profile:manage`
+  | `${OrganizationSystemPermissionPrefix}profile:delete`
+  | `${OrganizationSystemPermissionPrefix}memberships:read`
+  | `${OrganizationSystemPermissionPrefix}memberships:manage`
+  | `${OrganizationSystemPermissionPrefix}domains:read`;
 
 /**
  * OrganizationPermissionKey is a combination of system and custom permissions.
diff --git a/packages/types/src/session.ts b/packages/types/src/session.ts
index 028ceacee3..f62bf0d317 100644
--- a/packages/types/src/session.ts
+++ b/packages/types/src/session.ts
@@ -15,6 +15,7 @@ import type {
   OrganizationCustomPermissionKey,
   OrganizationCustomRoleKey,
   OrganizationPermissionKey,
+  OrganizationSystemPermissionPrefix,
 } from './organizationMembership';
 import type { ClerkResource } from './resource';
 import type {
@@ -25,6 +26,29 @@ import type {
 import type { TokenResource } from './token';
 import type { UserResource } from './user';
 
+type DisallowSystemPermissions<P extends string> = P extends `${OrganizationSystemPermissionPrefix}${string}`
+  ? 'System permissions are not included in session claims and cannot be used on the server-side'
+  : P;
+
+/**
+ * Type guard for server-side authorization checks using session claims.
+ * System permissions are not allowed since they are not included
+ * in session claims and cannot be verified on the server side.
+ */
+export type CheckAuthorizationFromSessionClaims = <P extends OrganizationCustomPermissionKey>(
+  isAuthorizedParams: WithReverification<
+    | {
+        role: OrganizationCustomRoleKey;
+        permission?: never;
+      }
+    | {
+        role?: never;
+        permission: DisallowSystemPermissions<P>;
+      }
+    | { role?: never; permission?: never }
+  >,
+) => boolean;
+
 export type CheckAuthorizationFn<Params> = (isAuthorizedParams: Params) => boolean;
 
 export type CheckAuthorizationWithCustomPermissions =