The relationship between habitual physical activity and pulmonary function were considered in 424 boys and 366 girls, 9–18 years of age. Indicators of habitual physical activity were assessed using a 3-day activity diary and included estimated daily energy expenditure (EE) and time spent in moderate-to-vigorous physical activity (MVPA) (METs ≥ 4.8). Pulmonary function was measured according to standard procedures. Relationships were examined with partial correlations and ANCOVA, comparing the highest and lowest quartiles of EE and MVPA. When age and stature are statistically controlled, relationships between EE, MVPA, and pulmonary function was generally low and not significant, with the exception of FEV1% in 16–18-year-old girls (r ≤ −0.28). Youth in the highest and lowest quartiles of EE and MVPA do not differ in pulmonary function, except for PEER in 9–12-year-old boys, and FEV1% in 16–18-year-old boys, which are slightly greater (1–3%) in the less active group. These findings indicate that lung volumes, capacities, and flow rates are not consistently related to estimated habitual physical activity in a general, free-living population of youth.