This paper introduces a predictive congestion pricing method in cities wherein the tolls alter from region to region. We consider a large urban network is partitioned into multiple regions each with a well-defined Macroscopic Fundamental Diagram (MFD) where multiple routes exist between each origin and destination regions. The proposed cordon pricing method is designed to (i) minimize vehicles’ total time spent in the network and (ii) aim for a revenue-neutral tolling. A controller based on model predictive control (MPC) approach is proposed to determine the (possibly negative) optimal time- and region-varying tolls. The MPC controller comprises a regional MFD-based traffic model with no need of destination information and a long-short term memory neural network (LSTM-NN) to obtain an accurate estimation of inter-region transfer flows. Results of numerical experiments indicate the effectiveness of the proposed congestion pricing method to achieve the two objectives simultaneously, compared with No toll and reactive feedback controllers.