Objectives This study aimed to investigate cross-lagged associations of leaping skill and throwing–catching skills with objectively measured moderate-to-vigorous physical activity (MVPA) and sedentary time (ST) during school transition from upper primary (Grade 6) to lower secondary school (Grade 7).

Design This study is a one-year prospective follow-up study within Finnish school settings. Students’ MVPA, ST, leaping skill and throwing–catching skills were measured at Grade 6 and subsequently at Grade 7.

Methods A sample of 336 students (163 girls, 173 boys; M age = 12.0 years, SD = 0.4 at Grade 6 participated in the study. Students’ MVPA and ST were measured objectively by hip-worn accelerometers. Leaping skill was measured by 5-leaps test. Throwing and catching skills were measured by throwing–catching combination test. Cross-lagged structural equation modeling was conducted to evaluate the associations between MVPA, ST, leaping skill, and throwing–catching skills at Grade 6 and Grade 7.

Results Results demonstrated three significant cross-lagged associations among girls: (1) leaping skill measured at Grade 6 was negatively associated with ST at Grade 7; (2) objectively measured MVPA at Grade 6 associated positively with leaping skill at Grade 7; and (3) throwing–catching skills measured at Grade 6 associated positively with leaping skill measured at Grade 7. There were no statistically significant cross-lagged associations between the study variables for the sample of boys.

Conclusions The results of this study indicated that supporting opportunities for girls’ engagement in both MVPA and leaping skill development activities during their primary school education is strongly recommended.