This research aims to highlight the evolution of the Portuguese and Romanian scientific system in the recent decades. This article presents the process of expansion of higher education in both countries, particularly at the level of the scientific system, trying to understand how scientific research in Portugal and Romania has evolved, as well as to know the sectors that conduct this activity. In this article, the authors support their analysis using Portuguese and Romanian official statistics and from international organizations, some indicators that can clarify the volume and quality of scientific research in these two countries between 2007 to 2019, analyzing the expansion of scientific research in the post-Bologna context. The article will be finished with two unifactorial regression models analysis. The main results of the study point towards that, for the period 2007-2019, in the higher education sector, a 1% growth in R&D expenditures leads, on average, to an increase in the number of researchers by 0.18% in Romania and 1.25% in Portugal. These results may help to formulate public policies conducive to improving the state of public higher education in Portugal and Romania, especially in the financing of postgraduate and scientific production.