This paper investigates the association between internal barriers to innovation and the propensity of technology-based SMEs to cooperate with universities and research institutes (URIs). We examine empirically two types of internal company barriers – financial and knowledge obstacles to innovation. The data source is the latest edition of the Brazilian Innovation Survey (PINTEC). We analyse the full sample of technology-based SMEs as well as the subsamples of high-tech manufacturing companies and knowledge-intensive business services (KIBS). Financial obstacles are shown to be strongly related to the propensity of KIBS to collaborate with URIs. Knowledge obstacles are moderately related to the propensity of high-tech manufacturing SMEs to collaborate with URIs. We conclude that while URIs have other important roles in the techno-economic system, their perceived contribution to alleviating internal innovation barriers for technology-based SMEs may be less prominent than policy decision-makers in emerging economies may expect.