Objectives This study aimed to determine through detailed contextual investigation the effects of seasonal resource shortages, and household and individual level differences, on child growth in rural Timor‐Leste. We compared trends in growth across two rural Timorese villages with different ecologies. Methods Heads of 104 households in Natarbora, Timor‐Leste, were interviewed and resource levels assessed during the food shortage season. In these households, 337 children were measured for height, weight, and mid‐upper arm circumference. World Health Organization standardized measures were calculated and compared with dry season measurements. Using hierarchical linear models, child growth was related to household resource levels. Results were then compared to data from rural mountainous Ossu, Timor‐Leste. Results z BMI declined over the wet season when food resources were scarce compared with the dry season (P < .001). Both age and sex were strong predictors of child growth, with older children having worse z height‐for‐age (P = .001) and z weight‐for‐age (P < .001) and boys shorter for age than girls (P = .049). Children were taller in households with modern flushable toilets (P = .005). Agricultural strategies such as crop diversity and land cultivation were linked to child growth. Results parallel findings from Ossu on the effects of season, child age and sex, but not household level socioeconomic differences. Conclusions Results highlight the importance of subsistence‐based resource stabilization and of early intervention to prevent growth faltering. Predicting growth using ecological models requires small‐scale investigation, as variation exists among rural areas within an ecologically and culturally diverse country.