Estimates of the components of nutrient intake variation are needed for modelling distributions of usual intake or predicting the usual intake of individuals. Season is a potential source of variation in nutrient intakes in addition to within- and between-person variation, particularly in low- or middle-income countries. We aimed to describe seasonal variation in nutrient intakes and estimate within-person, between-person and other major components of intake variance among Zambian children. Children from rural villages and peri-urban towns in Mkushi District, Zambia aged 4–8 years were enrolled in the non-intervened arm of a randomised controlled trial of pro-vitamin A carotenoid biofortified maize (n 200). Up to seven 24-h dietary recalls per child were obtained at monthly intervals over a 6-month period covering the late post-harvest (August–October), early lean (November–January) and late lean (February–April) seasons (2012–2013). Nutrient intakes varied significantly by season. For energy and most nutrients, intakes were highest in the early lean season and lower in the late post-harvest and late lean seasons. Season and recall on a market day had the strongest effects on nutrient intakes among covariates examined. Unadjusted within- to between-person variance ratios ranged from 4·5 to 31·3. In components of variance models, season accounted for 3–20 % of nutrient intake variance. Particularly in rural settings in low- and middle-income countries, where availability of locally grown, nutrient-rich foods may vary seasonally, studies should include replicates across seasons to more precisely estimate long-term usual intakes.