Innovation plays a crucial role in ensuring economic growth and competitiveness of national economies, creating conditions for their sustainable development. By focusing on supporting innovation, the EU is particularly helping to accelerate the development of those member states that lag far behind the EU average. This requires the selection of the indicators reflecting the development of innovation that determine the differences between member countries to the greatest extent. Therefore, the aim of the study is to identify the key factors of the innovation gap (FIG) between EU countries based on a comparison of indicators characterizing the national innovation systems (NIS). For this purpose, 22 relative indicators were selected from the indicators included in the Global Innovation Index to form an array of empirical data. At the first stage, the EU countries were divided into four clusters using the k-means method. At the second stage, using the decision tree method, a group of indicators was identified that together distinguish the obtained clusters to the greatest extent and, accordingly, determine the differences between EU countries and can be considered as FIG, namely: “Researchers”, “GERD financed by business”, “Joint venture/strategic alliance deals”, “Software spending”, and “High-tech manufacturing”. This allows individual member states to prioritize the development of those indicators (i.e. FIG) that most determine their position in the EU and therefore improve their NIS. At the EU level, this will contribute to the complementarity of the NIS, overcome differences between member states and increase the overall level of convergence in innovation.