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The purpose of this study was to empirically test a comprehensive conceptual model linking gross motor skills, school day physical activity and health-related variables in a sample of sixth graders. Participants were a convenience sample of 84 sixth grade students (Mean age = 11.6 &#177; 0.6 years). Gross motor skills were assessed using the Test of Gross Motor Development-3rd Edition (TGMD-3), school day physical activity was assessed using pedometers, health-related fitness was assessed using Progressive Aerobic Cardiovascular Endurance Run (PACER) laps, perceived competence assessed using a validated questionnaire and the health-related outcome was assessed using Body Mass Index (BMI). The relationship between school day step counts and TGMD-3 scores was mediated through both perceived competence and PACER laps (<i>p</i> = 0.015) and the direct path coefficient between TGMD-3 scores and BMI was statistically significant (<i>b</i> = &#8722;0.22 kg/m², <i>p</i> &lt; 0.001). Overall there was good model fit with all indices meeting acceptable criteria (<i>&#967;</i>² = 3.7, <i>p</i> = 0.293; Root Mean Square Error of Approximation (RMSEA) = 0.062, 90% Confidence Interval (C.I.): 0.00&#8315;0.23; Comparative Fit Index (CFI) = 0.98; Tucker-Lewis Index (TLI) = 0.96; Standardized Root Mean Square Residual (SRMR) = 0.052). The comprehensive conceptual model explaining the inter-relationships among motor competence and health-related variables was empirically validated with the relationship between physical activity and gross motor skills mediated through both perceived competence and cardiorespiratory endurance in a sample of sixth graders.