Background: Although previous studies have demonstrated that children with high levels of fundamental movement skill competency are more active throughout the day, little is known regarding children’s fundamental movement skill competency and their physical activity during key time periods of the school day (i.e., lunchtime, recess and after-school). The purpose of this study was to examine the associations between fundamental movement skill competency and objectively measured moderate-to-vigorous physical activity (MVPA) throughout the school day among children attending primary schools in low-income communities. Methods: Eight primary schools from low-income communities and 460 children (8.5 ± 0.6 years, 54% girls) were involved in the study. Children’s fundamental movement skill competency (TGMD-2; 6 locomotor and 6 object-control skills), objectively measured physical activity (ActiGraph GT3X and GT3X + accelerometers), height, weight and demographics were assessed. Multilevel linear mixed models were used to assess the cross-sectional associations between fundamental movement skills and MVPA. Results: After adjusting for age, sex, BMI and socio-economic status, locomotor skill competency was positively associated with total (P = 0.002, r = 0.15) and after-school (P = 0.014, r = 0.13) MVPA. Object-control skill competency was positively associated with total (P < 0.001, r = 0.20), lunchtime (P = 0.03, r = 0.10), recess (P = 0.006, r = 0.11) and after-school (P = 0.022, r = 0.13) MVPA. Conclusions: Object-control skill competency appears to be a better predictor of children’s MVPA during school-based physical activity opportunities than locomotor skill competency. Improving fundamental movement skill competency, particularly object-control skills, may contribute to increased levels of children’s MVPA throughout the day.Trial registrationAustralian New Zealand Clinical Trials Registry No: ACTRN12611001080910.