Despite broad implications for understanding human life history, energetics, and health, the impact of physical activity on childhood growth remains unclear. Particularly understudied is the effect of secular changes in physical activity on child development. We address these shortcomings using data spanning the transition from traditional to semi-developed economy among Yucatec Maya agriculturalists. Anthropometric and behavioral observation data were collected from children living in a subsistencebased rural community in 1992 and again in 2012 following the introduction of a school and mechanized technologies but minimal overt dietary change. Multiple regression analyses demonstrate dramatic twenty-year transformations in how children spent their time. This behavioral change was associated with large declines in estimated physical activity level (PAL), associated activity energy expenditure savings of several hundred kilocalories/day, and sizable increases in mean height, weight, and triceps skinfold thickness. Controlling for observed frequency of market food consumption, PAL was inversely related to child body size and subcutaneous fat stores and significantly mediated the effects of data collection year on anthropometric indices. These findings indicate that physical activity can considerably influence childhood growth, highlighting the role of energy allocation tradeoffs between physical activity and competing life tasks in shaping patterns of human ontogeny and health.