The urban public transportation system is an essential element of our cities and requires efficient transit network design to provide high-quality service to passengers. The quality of the transit network directly impacts the directness of passengers, as well as the profitability of the transportation company. The purpose of our paper is to introduce a novel method for addressing the challenges associated with the Transit Network Design and Frequency Setting Problem (TNDFSP). A number of optimization techniques have been proposed for TNDFSP, with previous approaches often relying on a sequential optimization approach that tackles transit network design and service frequency setting as separate tasks. In contrast, our new algorithm takes a simultaneous optimization approach leveraging graph neural networks and deep reinforcement learning to optimize passenger benefits, operating costs, and service frequencies. We test the proposed algorithm on the popular Mandl Swiss network and produce highly competitive results.