The purpose of this study was to examine changes in physique and motor skills among young children enrolled in a private kindergarten based in Osaka City (K Kindergarten) from fiscal years 2016 to 2020, including the period when COVID-19 was prevalent. Anthropometric measurements (height and weight) and results from five motor skills activities (25-meter run, standing long jump, tennis ball throw, continuous two-footed jump, and sustained body support) were recorded annually throughout each child’s three-year enrollment period. Longitudinal data collected from 323 children was analysed. K Kindergarten has been assessing motor skills for about 35 years and continued this practice throughout the COVID-19 pandemic. During the 2020-2022 school years, caregivers conducted research on the theme "physical activity to nurture a rich mind and strong body" and implemented environmental structures for physical activity. Analysis of changes in body size and athletic ability by year of enrollment revealed that children who entered preschool in the 2018 school year, transitioning from middle to upper grades during the COVID-19 pandemic, had significantly higher body weight values compared to other years. The results also indicated that girls were more likely than boys to be affected by activity restrictions and the childcare environment regarding their physique and motor skills during early childhood. Moreover, children who entered preschool in 2019 and 2020 and engaged in a motor play environment showed significantly higher motor skills scores when enrolled in the upper grades. These findings suggest that, despite the various limitations imposed by COVID-19, the inclusion of motor play positively influenced the motor skills of young children.