Social and school closures during the COVID-19 pandemic may have led to significant stagnation in children’s motor development, but precise data on this are lacking. We aimed to examine the impact of the pandemic and society closure on motor development of school children and to find differences between rural and urban environments. From the SLOfit database, we obtained anonymous results from 756 6th grade children before the pandemic ( 11.3 ± 0.5 years, 52.5% boys) who performed physical fitness measurements in 2017 and 2019 in 8th grade and from 853 6th grade children ( 11.4 ± 0.5 years, 51% boys) who performed measurements in 2019 and 2021, after 3 pandemic waves. The results of eight physical activity tests and the overall physical fitness index were compared between the prepandemic and the pandemic generation. We divided the sample into four groups (rural and urban prepandemic group and rural and urban pandemic group) and compared the changes in test scores between 6th and 8th grade. We found a statistically significant decrease in the physical fitness index of the pandemic generation (from 51.6 ± 29.6 to 45.8 ± 30.3 ) compared to the prepandemic generation (from 50.4 ± 30.5 to 50.5 ± 29.7 ), p < 0.001 . The greatest effects of pandemic closure were found in the 600-meter run, in polygon course backwards test, in the number of sit-ups in 60 seconds, and in the 60-meter sprint. Children from rural areas showed worse decrement in physical fitness index compared to urban areas, except for 600-meter run. We conclude that the pandemic closure has had a significant inhibitory effect on the motor development of schoolchildren and has reduced their overall physical fitness with worse decline in rural areas. The pandemic generation of children needs more physical education in schools and other systemic interventions to mitigate these consequences.