This paper presents a Graphics Processing Unit (GPU) acceleration of an iteration-based discrete velocity method (DVM) for gas-kinetic model equations. Unlike the previous GPU parallelization of explicit kinetic schemes, this work is based on a fast converging iterative scheme. The memory reduction techniques previously proposed for DVM are applied for GPU computing, enabling full three-dimensional (3D) solutions of kinetic model equations in the contemporary GPUs usually with a limited memory capacity that otherwise would need terabytes of memory. The GPU algorithm is validated against the direct simulation Monte Carlo (DSMC) simulation of the 3D lid-driven cavity flow and the supersonic rarefied gas flow past a cube with the phase-space g...