Motor skills are needed for physical development and may be linked to health-related fitness and physical activity levels. No studies have examined the relationships among these constructs in large samples of disadvantaged children from low-income families using the Test for Gross Motor Development–3rd Edition (TGMD-3). The purpose of this study was to examine the multivariate associations among health-related fitness, physical activity, and motor skills assessed using the TGMD-3. Participants included 1460 school-aged children (730 boys, 730 girls; M age = 8.4 years, SD = 1.8 years) recruited from the K to sixth grades from three low-income schools. Health-related fitness was assessed using the FITNESSGRAM battery, physical activity was assessed using accelerometers and pedometers, and motor skills were assessed using the TGMD-3. Canonical correlations revealed statistically significant correlations between the Ball Skills and health-related fitness variates (Rc = 0.43, Rc2 = 17%, p < 0.001). Significant canonical coefficients in the Ball Skills variate included two-handed striking, dribbling, and catching, and significant canonical coefficients in the health-related fitness variate included body mass index and the progressive aerobic cardiovascular endurance run (p < 0.01). Locomotor skills did not significantly correlate with health-related fitness or physical activity. Ball skills are related to health-related fitness in disadvantaged children from low-income families.