This disclosure relates generally to method and system for tuning graphics processing unit (GPU) parameters of a GPU kernel. The disclosure proposes a combination of both heuristic and deterministic techniques for tuning GPU parameters of a GPU kernel to achieve optimal configuration of the GPU parameters. The proposed method and a system for tuning GPU parameters is based on deterministic techniques and heuristic techniques that includes capturing behavior of the GPU application by monitoring several GPU hardware counters that comprise several hardware resources and performance counters. The proposed tuning GPU parameters also implements a set of heuristic techniques to decide course of the tuning for various GPU parameters based on the captured behaviour of the GPU hardware counters.