Adverse effects of prenatal mercury exposure on pregnancy outcomes remain a public health concern. We assessed the relationship between prenatal mercury exposure and newborn anthropometric characteristics in 334 mother-child pairs from the early stages of pregnancy to delivery in Tokyo, Japan, between December 2010 and October 2012. We found a negative correlation between blood mercury levels during the first and second trimesters of gestation and birth weight (r = -0.134 and -0.119, respectively; p < 0.05). Multiple linear regression analysis confirmed the relationship between first-trimester maternal blood mercury levels and birth weight when adjusted for independent variables (β = -0.170, t = -2.762; p = 0.006). Mean mercury levels in umbilical cord blood were twice as high as maternal blood levels (10.15 ± 7.74 and 4.97 ± 3.25 μg/L, respectively; r = 0.974, p < 0.001). Our findings suggest that pregnant women and women of reproductive age should avoid mercury exposure, even at low levels, because of its potentially adverse effects on fetal development.