Background: Unplanned pregnancy is a public health issue with adverse consequences for maternal and neonatal health. In Japan, the prevalence of unplanned pregnancy was 46.2% in 2002. However, few studies have investigated this topic, and there is little recent data from Japan. We described and examined the prevalence and determinants of unplanned pregnancy among rural women in Japan from 2011 to 2016. Methods: We used cross-sectional data from a community-based cohort study (Project Koshu). Data were collected from 2011 to 2016 via a self-report questionnaire included in the Maternal and Child Health Handbook of Japan. Pregnancy intention was measured as a binary variable (planned or unplanned). Univariate and multivariate logistic regression analyses were performed to examine factors associated with unplanned pregnancy, with results reported as odds ratios (ORs) and 95% confidence intervals (CIs). We conducted sensitivity analyses with different definitions of pregnancy intention to assess the robustness of the results. The significance level was set at 5%. Results: Of the 932 participants (mean ± standard deviation age at baseline: 31.3 ± 5.2 years), 382 (41%) pregnancies were reported as unplanned. The multivariate analyses showed that maternal age (+ 1 year: OR = 0.94, 95% CI: 0.92-0.97, p < 0.001), 'other' family structure (OR = 2.76, 95% CI: 1.12-6.76, p = 0.03), three or more pregnancies (OR = 2.26, 95% CI: 1.66-3.08, p < 0.001), current smoking (OR = 2.60, 95% CI: 1.26-5.35, p = 0.01), balanced diet (OR = 0.62, 95% CI: 0.47-0.83, p < 0.001) and current depression (OR = 1.63, 95% CI: 1.24-2.16, p < 0.001) were strongly associated with unplanned pregnancy. These associations were consistent across definitions of pregnancy intention, supporting the robustness of our results.