Low-level mercury (Hg) exposure in infancy might be harmful to the physical growth as well as neurodevelopment of children. The aim of this study was to investigate postnatal Hg exposure and its relationship with anthropometry and dietary factors in late infancy. We recruited 252 healthy Korean infants between six and 24 months of age from an outpatient clinic during the 2009/2010 and 2013/2014 seasons. We measured the weight and height of the infants and collected dietary information using questionnaires. The Hg content of the hair and blood was assessed using inductively coupled plasma mass spectroscopy. The geometric mean Hg concentration in the hair and blood was 0.22 (95% confidence interval: 0.20–0.24) µg/g and 0.94 (n =
109, 95% confidence interval: 0.89–0.99) µg/L, respectively. The hair Hg concentration showed a good correlation with the blood Hg concentration (median hair-to-blood Hg ratio: 202.7, r = 0.462, p
< 0.001) and was >1 µg/g in five infants. The hair Hg concentration showed significant correlations with weight gain after birth (Z-score of the weight for age—Z-score of the birthweight; r = −0.156, p
= 0.015), the duration (months) of breastfeeding as the dominant method of feeding (r = 0.274, p
< 0.001), and the duration of fish intake more than once per week (r = 0.138, p
= 0.033). In an ordinal logistic regression analysis with categorical hair Hg content (quartiles), dietary factors, including breastfeeding as the dominant method of feeding in late infancy (cumulative odds ratio: 6.235, 95% confidence interval: 3.086–12.597, p
< 0.001) and the monthly duration of fish intake more than once per week (cumulative odds ratio: 1.203, 95% confidence interval: 1.034–1.401; p
= 0.017), were significantly associated with higher hair Hg content. Weight gain after birth was not, however, significantly associated with hair Hg content after adjustment for the duration of breastfeeding as the dominant method of feeding. Low-level Hg exposure through breastfeeding and fish intake as a complementary food did not directly affect anthropometry in this population. If prolonged breastfeeding is expected, however, the Hg exposure through fish intake may need to be monitored for both mothers and infants.