The aim of this study was to identify child and school-level characteristics that explained inter-individual differences in gross motor coordination (GMC). Participants (n = 390), recruited from 18 Portuguese primary schools, were aged 6 to 10 years of age. Birth weight, body fat (BF), physical activity (PA), physical fitness (PF) and GMC were assessed. School size, setting, infrastructure and physical education classes were considered as school context markers. A multilevel modeling approach was used to identify hierarchical effects (child and school levels). It was found that children-level variables (sex, PF, and BF) significantly explained 63% of the 90% variance fraction at the individual level; boys outperformed girls (p < 0.05), individuals with higher BF were less coordinated (p < 0.05), and those with higher PF were more coordinated (p < 0.05). School-variables (e.g. school size and playing surface) explained 84% of the 10% variation fraction. These findings confirm the roles of sex, PFS and BF. Interestingly they also suggest that the school environment plays a minor but significant role in GMC development. However, it is important to stress that the school context and conditions can also play an important role in a child's motor development, providing adequate and enriching motor opportunities.