Children’s motor competence (MC) has declined in the past decades, while sedentary behavior (SB) has increased. This study examined the association between MC and physical activity (PA) levels among primary schoolchildren. Demographics, body height and weight, MC (Athletic Skills Track) and PA levels (ActiGraph, GT3X+) were assessed among 595 children (291 boys, mean age = 9.2 years, SD = 1.1). MC was standardized into five categories: from very low to very high. PA levels were classified into sedentary behavior (SB), light physical activity (LPA), and moderate-to-vigorous physical activity (MVPA). Mixed model analyses were conducted with PA levels as dependent variables and MC as the independent variable, while adjusting for age, gender, and BMI z-score on the individual level. Additional moderation analyses between covariates and MC and PA levels were also conducted. A negative association between MC and SB (β = -3.17) and a positive association between MC and MVPA (β =1.41) were found. The strength of both associations increased as children expressed lower or higher levels of MC. Increased age and being a girl were significant predictors of higher levels of SB and lower levels of MVPA. Non-overweight children spent significantly more minutes in MVPA compared with overweight children. No moderating effects of BMI, gender, and age were found on the association between MC and PA levels. MC is an important correlate of both SB and MVPA, particularly for children with very high or low MC. Developing and improving children’s MC may contribute to spending less time in SB and more time in MVPA, particularly for high-risk groups, i.e. children with low MC. Moreover, addressing MC development and PA promotion simultaneously might create positive feedback loops for both children’s MC and PA levels.