Background: A growing number of studies have sought to examine the health associations of workplace social capital; however, evidence of associations with overweight is sparse. We examined the association between individual perceptions of workplace social capital and overweight among Japanese male and female employees.Methodology/Principal Findings: We conducted a cross-sectional survey among full-time employees at a company in Osaka prefecture in February 2012. We used an 8-item measure to assess overall and sub-dimensions of workplace social capital, divided into tertiles. Of 1050 employees, 849 responded, and 750 (624 men and 126 women) could be linked to annual health check-up data in the analysis. Binomial logistic regression models were used to calculate odds ratios and 95% confidence intervals for overweight (body mass index: >= 25 kg/m(2), calculated from measured weight and height) separately for men and women. The prevalence of overweight was 24.5% among men and 14.3% among women. Among men, low levels of bonding and linking social capital in the workplace were associated with a nearly 2-fold risk of overweight compared to high corresponding dimensions of social capital when adjusted for age, sleep hours, physiological distress, and lifestyle. In contrast, among women we found lower overall and linking social capital to be associated with lower odds for overweight even after covariate adjustment. Subsequently, we used multinomial logistic regression analyses to assess the relationships between a 1 standard deviation (SD) decrease in mean social capital and odds of underweight/overweight relative to normal weight. Among men, a 1-SD decrease in overall, bonding, and linking social capital was significantly associated with higher odds of overweight, but not with underweight. Among women, no significant associations were found for either overweight or underweight.Conclusions/Significance: We found opposite gender relationships between perceived low linking workplace social capital and overweight among Japanese employees.