In rural agricultural communities in Africa, particularly those with a single annual harvest, the preharvest period has been associated with increased food insecurity. We estimated the association between seasonal food insecurity and childhood malnutrition in Haydom, Tanzania. Children enrolled in a birth cohort study were followed twice weekly to document food intake and monthly for anthropometry until the age of 2 years. Household food insecurity was reported by caregivers every 6 months. We modeled the seasonality of food insecurity and food consumption, and estimated the impact of birth season on enrollment weight and subsequent malnutrition. Finally, we described the seasonality of admissions for acute malnutrition at a local referral hospital (Haydom Lutheran Hospital) from 2010 to 2015. Food insecurity was highly seasonal, with a peak from December to February. Children born during these 3 months had an average 0.35 z-score (95% CI: 0.12, 0.58) lower enrollment weight than children born in other months. In addition, weight-for-length z-scores measured in these months were on average 0.15 z-scores lower (95% CI: 0.10, 0.20) than that in other months, adjusting for enrollment weight and seasonal infectious diseases, and this disparity was sustained up to the age of 2 years. Correspondingly, the number of admissions with acute malnutrition at the local hospital was highest at this time, with twice as many cases in December-February compared with June-August. We identified acute and chronic malnutrition associated with seasonal food insecurity and intake. Targeting of prenatal care and child-feeding interventions during high food insecurity months may help reduce child malnutrition.