Lymphocytic choriomeningitis virus (LCMV) is a neglected rodent-borne zoonotic virus primarily infecting house mice. The virus can be highly pathogenic, particularly in immunocompromised individuals and in congenital infections. LCMV is distributed worldwide but shows local clustering, probably due to the highly structured populations of its hosts and the vertical transmission of the pathogen. These factors should also promote long-term virus persistence in wild populations, yet this aspect remains largely unexplored. To investigate this, we resampled a transect in the western Czech Republic that was primarily studied more than a decade ago. Additionally, we analyzed a sample collection from Buškovice, a locality where LCMV was first detected in 2008, to trace virus presence back to the year 2000. Positive samples underwent whole-genome characterization to assess the virus’s genetic structure over space and time. We detected intermittent presence over 24 years in a geographically limited area, where LCMV was already present in 2000 and remained detectable in 2023. Phylogenetic analysis showed no clear spatio-temporal clustering, suggesting that virus persistence in Buškovice is a dynamic process involving mouse dispersal between neighboring villages. Given LCMV’s zoonotic potential and house mouse synanthropy, these findings highlight the need for continuous monitoring in the region.