The relationship between high body mass index (BMI) >25 kg/m2 and risk for stillbirth in the Japanese population remains unclear. This study aimed to estimate the impact of maternal obesity on the risk of stillbirth in a Japanese population. This prospective cohort study used data from the Japan Environment and Children’s Study, which recruited pregnant individuals between 2011 and 2014. A total of 93,772 fetuses were considered eligible for inclusion in this study. Stillbirth (fetal death before or during labor at ≥22 completed weeks of gestation) rates were compared among four pre-pregnancy BMI groups: underweight (<18.5 kg/m2), reference (18.5 to <25.0 kg/m2), overweight (25.0 to <30.0 kg/m2), and obese (≥30.0 kg/m2). The association between pre-pregnancy BMI and the risk of stillbirth was estimated using multiple logistic regression analyses. The overall stillbirth incidence was 0.33% (305/93,722). Compared with the reference group, the risk of stillbirth was significantly higher in the overweight group (adjusted odds ratio [aOR]: 1.55; 95% confidence interval [CI]: 1.08–2.23) and the obese group (aOR: 2.60; 95% CI: 1.59–4.24). The overall incidence of early stillbirth (i.e., <28 weeks) was 0.17% (155/93,722). Similarly, after adjusting for potential confounding factors, the risk of early stillbirth was significantly higher in the obese group (aOR: 4.33; 95% CI: 2.44–7.70). Increased maternal BMI was associated with an increased risk of stillbirth in the Japanese population. Therefore, counselling women planning for pregnancy on the importance of an appropriate pre-pregnancy BMI to minimize the risk of stillbirth is important.