This paper aims to deepen our understanding of how migration shapes the socio-demographic structure of the peripheral rural regions. We bridge the fields of peripherality and migration research to address the gap in understanding their interplay. We use Lithuania as a case study, exemplifying the metropolization-peripheralization trend and selective migration patterns. Our analysis uses a unique longitudinal, geocoded data set covering the entire population, including inner and international migrants, allowing for a detailed examination of migration patterns across spatial and temporal dimensions from 2001 to 2021. The results show significant variations in the characteristics of individuals migrating to and from peripheral rural regions across different directions, with two-way migration flows playing an important role in shaping the socio-demographic structure of these regions. Furthermore, migration—particularly inner migration—has become an increasingly important factor influencing population dynamics and contributing to further peripheralization.