Maternal prenatal psychological distress, including depression and anxiety, may affect offspring’s motor/cognitive development. However, research findings have been inconsistent. We used a dataset from the Japan Environment and Children’s Study to evaluate associations between maternal six-item Kessler Psychological Distress Scale (K6) scores and motor/cognitive development among offspring at two years of age. Their offspring’s motor/cognitive development was assessed using the Kyoto Scale of Psychological Development 2001. Records for 1859 male and 1817 female offspring were analyzed. The maternal K6 was administered twice during pregnancy: at a median of 14.6 weeks (M-T1) and 27.3 weeks (M-T2) of gestation. Multiple regression analysis was performed with the group with K6 scores ≤4 at both M-T1 and M-T2 as a reference. In the group with K6 scores ≥5 at both M-T1 and M-T2, male offspring had significantly lower developmental quotients (DQ) in the posture-motor area (partial regression coefficient [B]: −3.68, 95% confidence interval [CI]: −5.92 to −1.44) and language-social area (B: −1.93; 95%CI: −3.73 to −0.12), while female offspring had a lower DQ for the language-social area (B: −1.95; 95%CI: −3.73 to −0.17). In those with K6 scores ≥5 only at M-T1 or M-T2, male and female offspring did not differ significantly in DQ for any area. Continuous maternal psychological distress from the first to the second half of pregnancy was associated with lower motor and verbal cognitive development in male offspring and lower verbal cognitive development in female offspring at 2 years compared with the group without persistent maternal prenatal psychological distress.