Intellectual capital is one of the most crucial determinants of long-term economic development. The countries compete for highly skilled labor and talented youth. State regulatory interventions aim to, on the one hand, facilitate the retention of foreign high-productivity intellectual capital in the host country, transforming ‘educational’ and ‘scientific’ migrants into residents, and on the other hand, prevent the outflow of their own qualified workforce. The paper aims to outline the role of the nation’s higher education system in the influx and outflow of labor resources. A two-stage approach is applied: 1) maximum likelihood—to cluster the EU countries and the potential candidates to become members of EU countries based on the integrated competitiveness of their higher education systems, considering quantitative, qualitative, and internationalization aspects; 2) logit and probit models—to estimate the likelihood of net migration flow surpassing baseline cluster levels and the probability of migration intensity changes for each cluster. Empirical findings allow the identification of four country clusters. Forecasts indicate the highest likelihood of increased net migration flow in the second cluster (66.7%) and a significant likelihood in the third cluster (23.4%). However, the likelihood of such an increase is statistically insignificant for countries in the first and fourth clusters. The conclusions emphasize the need for regulatory interventions that enhance higher education quality, ensure equal access for migrants, foster population literacy, and facilitate lifelong learning. Such measures are imperative to safeguard the nation’s intellectual potential and deter labor emigration.