Abstract Analytical models used for latency estimation of Network-on-Chip (NoC) are not producing reliable accuracy. This makes these analytical models difficult to use in optimization of design space exploration. In this paper, we propose a learning based model using deep neural network (DNN) for latency predictions. Input features for DNN model are collected from analytical model as well as from Booksim simulator. Then this DNN model has been adopted in mapping optimization loop for predicting the best mapping of given application and NoC parameters combination. Our simulations show that using the proposed DNN model, prediction error is less than 12% for both synthetic and application specific traffic. More than 108 times speedup could be achieved using DPSO with DNN model compared to DPSO using Booksim simulator.