Aflatoxins are toxic metabolites of Aspergillus molds and are widespread in the food supply, particularly in low‐ and middle‐income countries (LMICs). Both in utero and infant exposure to aflatoxin B1 (AFB1) have been linked to poor child growth and development. The objective of this prospective cohort study was to investigate the association between maternal aflatoxin exposure during pregnancy and adverse birth outcomes, primarily lower birth weight, in a sample of 220 mother‐infant pairs in Mukono district, Uganda. Maternal aflatoxin exposure was assessed by measuring the serum concentration of AFB1‐lysine (AFB‐Lys) adduct at 17.8 ± 3.5 (mean ± SD) weeks gestation using high performance liquid chromatography (HPLC). Anthropometry and birth outcome characteristics were obtained within 48 hours of delivery. Associations between maternal aflatoxin exposure and birth outcomes were assessed using multivariable linear regression models adjusted for confounding factors. Median maternal AFB‐Lys level was 5.83 pg/mg albumin (range: 0.71‐95.60 pg/mg albumin, IQR: 3.53‐9.62 pg/mg albumin). In adjusted linear regression models, elevations in maternal AFB‐Lys levels were significantly associated with lower weight (adj‐β: 0.07; 95% CI: ‐0.13, ‐0.003; p = 0.040), lower weight‐for‐age Z‐score (adj‐β: ‐0.16; 95% CI: ‐0.30, ‐0.01; p = 0.037), smaller head circumference (adj‐β: ‐0.26; 95% CI: ‐0.49, ‐0.02; p = 0.035), and lower head circumference‐for‐age Z‐score (adj‐β: ‐0.23; 95% CI: ‐0.43, ‐0.03; p = 0.023) in infants at birth. Overall, our data suggest an association between maternal aflatoxin exposure during pregnancy and adverse birth outcomes, particularly lower birth weight and smaller head circumference, but further research is warranted.