Effective innovative systems testify to the success of regional economic policies. Based on the neoclassical approach novel approach towards evalution of regional innovation system functioning is suggested. In this study, the performance indicators of innovative systems in the regions of Kazakhstan are calculated using the non-parametric Data Envelopment Analysis (DEA) method for a convex model, with constant and variable effects of scale, focused on maximum outputs and minimum resource costs. The obtained results will facilitate providing recommendations for improving economic policy for the purposes of more efficient use of resources in regional innovation activities.