The development of innovation at a regional level in a transition economy is characterised by complex multidirectional processes of generating and commercialising innovation, indicating the need for systematic research and rethinking of the existing methods of managing such territorial entities to stimulate innovation. For the successful introduction and implementation of innovative solutions, the deployment of appropriate amounts of intellectual, material and financial resources as well as their concentration in space and time is important. This article aims to develop a model for assessing the effectiveness of regional innovation systems (RISs) during the shift from the transition economy to the market economy. The authors developed a two-stage data envelopment analysis (DEA) model connected with patent activities and the output of innovative goods and services. The model’s application made it possible to build maps describing the rating of regions concerning the performance indicator and to identify the availability of unutilised resources. For example, we identified efficient and inefficient regions in terms of producing innovative products, which is especially important for developing additional measures for developing the institutional environment of regions with considerable resources but very low utilisation efficiency. The data obtained will allow for more effective management of the structural elements of RISs as well as the detection of changes in the dynamics of key development indicators by identifying the size of efficiency reserves and the causes of their occurrence at the individual subject level.