The efficiency of the national innovation system (NIS) is widely considered to be the most important factor of innovation-based economic growth. Using the wide spectrum of different metrics for measuring the efficiency of NIS, modern studies focus mainly on high-income or upper-middle-income countries, while the effectiveness of the NIS in post-Soviet countries has not been studied enough. The post-socialist transformation has led to different models of economic development in these countries, which can be divided into three groups: a group with developed European institutions, a group with a focus on the European path of development, and, finally, a group of countries with an economic model of “state capitalism”. These models formed the trajectory of innovative development. The main purpose of this study is to compare the performance of NIS in post-Soviet countries and to find out whether differences between development institutions can help explain differences in the performance of NIS. The study applies the DEA methodology and considers NISs as homogeneous economic agents, which transform the same types of inputs (knowledge gained using human and financial resources) into the same types of positive outcomes (innovative products and services). The results of a study conducted on data for the period 2011–2018 show that there is no evidence to support the hypothesis that EU institutions or the type of economic model of the country directly relate to the effectiveness of the NIS. The example of Kazakhstan shows that NIS can be effective, even with strong state intervention in the economy. Taken together, the results of the paper suggest that the structure of R&D expenditures by sources of funding and types of research plays an important role in the formation of effective NIS.