This study investigates a design optimization of a rotating two-pass rectangular cooling channel with staggered arrays of pin-fins. The radial basis neural network method is used as an optimization technique with Reynolds-averaged Navier-Stokes analysis of fluid flow and heat transfer with shear stress transport turbulent model. The ratio of the diameter to height of the pin-fins and the ratio of the streamwise spacing between the pin-fins to height of the pin-fin are selected as design variables. The optimization problem has been defined as a minimization of the objective function, which is defined as a linear combination of heat transfer related term and friction loss related term with a weighting factor. Results are presented for streamlines, velocity vector fields, and contours of Nusselt numbers, friction coefficients, and turbulent kinetic energy. These results show how fluid flow in a two-pass square cooling channel evolves a converted secondary flows due to Coriolis force, staggered arrays of pin-fins, and a $180^{circ}$ turn region. These results describe how the fluid flow affects surface heat transfer. The Coriolis force induces heat transfer discrepancy between leading and trailing surfaces, having higher Nusselt number on the leading surface in the second pass while having lower Nusselt number on the trailing surface. Dean vortices generated in $180^{circ}$ turn region augment heat transfer in the turning region and in the upstream region of the second pass. As the result of optimization, in comparison with the reference geometry, thermal performance of the optimum geometry shows the improvement by 30.5%. Through the optimization, the diameter of pin-fin increased by 14.9% and the streamwise distance between pin-fins increased by 32.1%. And, the value of objective function decreased by 18.1%.