Abstract This research analyzes the scientific production of Chilean universities for the period 2013-2017 using a balanced panel data. The methodology uses an aggregate production function of the Cobb-Douglas type solved by means of a fixed effects panel data model, a Stochastic Frontier Analysis (SFA). The main results show that the models are equivalent and complementary in their analysis -They quantify the impact of financial resources and advanced human capital. The fixed effects model shows that the Chilean university system experiences increasing returns to scale, and the SFA model showed important efficiency gaps among universities. These results are relevant, since the models allow the follow-up and monitoring of public investment, of hiring programs by HEIs, and finally, the adequacy of public policies towards Science and Technology