Maternal dietary quality may alter the nutrient content of breast milk. In this study, we aimed to investigate the relationship between the healthy eating index (HEI) and alternative healthy eating index (AHEI) of a breastfeeding mother’s diet with the antioxidant profile of her breast milk and her infant’s urine. This study included 300 healthy mother-infant pairs. The participants’ dietary intake was estimated using a validated semi-quantitative food frequency questionnaire. The diet quality of participants was assessed using the HEI and AHEI. The total antioxidant content of the breast milk and infant’s urine was evaluated using ferric reducing antioxidant power (FRAP), 2, 2′-diphenyl-1-picrylhydrazyl (DPPH), thiobarbituric acid reactive substances (TBARs), and Thiol quantification assays. After adjusting for confounding factors, the odds of a low malondialdehyde (MDA) content of breast milk were significantly higher in the highest quartile of HEI than in the lowest quartile. The odds of low DPPH and FRAP in infant urine decreased in the highest quartile of HEI compared to the lowest quartile. No significant relationship was found between AHEI and antioxidant levels of breast milk and the infant’s urine. Our findings demonstrate that a high quality diet of breastfeeding mothers, identified by a higher HEI, can affect the oxidant-antioxidant balance of a mother’s breast milk and her infant’s urine.