The European hare is a rapidly declining farmland specialist, particularly sensitive to changes in landscape structure and agricultural management. Previous studies had found that agricultural landscape diversity can affect population densities; however, this evidence came from distant locations with different environmental and climatic conditions. Therefore, the main aim of this study was to assess the differences in European hare population densities between two neighboring locations (1.1 km apart) in Czechia, with contrasting landscape structures and compositions (heterogeneous vs. homogeneous study areas), and to compare these with a control study area featuring small-scale farming in Lower Austria. The European hare population densities were determined using infrared thermography in regular squares with fixed line transects during two spring monitoring periods in Czechia and one in Austria (2023–2024). We found significantly higher adult densities in the Czech heterogeneous landscape during two spring monitoring periods in 2023 and 2024 (117.3 ± 68.1 to 179.0 ± 95.4 ind./100 ha). A comparable population density was found in Austria (90.6 ± 50.0 to 113.8 ± 48.6 ind./100 ha). Contrarily, we found an incomparably lower population density in the Czech neighboring homogeneous landscape (25.0 ± 29.7 to 38.3 ± 44.1 ind./100 ha) and an even more contrasting pattern was found for subadults and juveniles. Detected population density of juveniles was 7.0 ± 10.6 to 24.3 ± 24.7 ind./100 ha in a Czech heterogeneous landscape, 8.1 ± 10.6 to 11.9 ± 12.0 ind./100 ha in Austria, but only 0.4 ± 1.6 to 2.1 ± 5.6 ind./100 ha in a Czech homogeneous landscape, which may indicate a lower survival rate in homogeneous agroecosystems. Our findings, based on pair comparison of neighboring areas with comparable environmental and climatic factors but with contrasting farmland structures and agricultural practices, suggest that population density is primarily driven by agroecosystem quality (i.e., heterogeneous small-scale farmland with a higher share of non-agricultural vegetation).