To examine the relationships among school day sedentary times (SED), light physical activity (LPA), and moderate to vigorous physical activity (MVPA) with gross motor skills in children using Compositional Data Analysis.Participants were 409 children (mean age = 8.4 [1.8] y) recruited across 5 low-income schools. Gross motor skills were assessed using the test for gross motor development—third edition (TGMD-3), and physical activity was assessed using accelerometers. Isometric log-ratio coordinates were calculated by quantifying the relative proportion of percentage of the school day spent in SED, LPA, and MVPA. The associations of the isometric log-ratio coordinates with the TGMD-3 scores were estimated using general linear mixed-effects models adjusted for age, body mass index, estimated aerobic capacity, and school affiliation.A higher proportion of the school day spent in %MVPA relative to %SED and %LPA was significantly associated with higher TGMD-3 total scores (γMVPA = 14.44, P = .01). This relationship was also observed for the ball skills subtest scores (γMVPA = 16.12, P = .003).Replacing %SED and %LPA with %MVPA during school hours may be an effective strategy for improving gross motor skills, specifically ball skills, in low-income elementary school-aged children.