This article is devoted to the analysis of the impact of socio-economic shocks on the dynamics of higher education development. It is substantiated that, on the one hand, higher education influences the development of society and the economy, on the other hand, the development trends of a country provide both opportunities and limitations for its development. An algorithmic model for studying the impact of social and economic shocks on the development of the higher education system (HES) has been developed. To diagnose the relationship between higher education and the socio-economic development of Ukraine and Slovakia, the following indicators were used: GDP per capita, the Human Development Index, school enrollment, tertiary, and net migration. The presence of nonlinear trends in the change in indicators has been shown and portraits of the socio-economic development of the countries have been constructed. To assess the impact of socio-economic shocks on the HES, the time-series decomposition method and cross-spectral analysis were used. The time-series decomposition allowed us to identify cyclical components of indicators, based on applying cross-spectral analysis, and the most significant local harmonics and the lag of their influence on the occurrence of shocks in the HES were determined. The use of the developed models allows us to predict periods of shock points in the HES depending on shocks in the tendencies of GDP per capita and net migration.