This study examined the relationship between cognitive/structural social capital and post-traumatic stress disorder (PTSD) among victims of heavy rain and flood. Participants were individuals aged≥18 years affected by the July 2018 heavy rainfall in the cities of Kurashiki and Soja, Japan, and living in temporary housing. We distributed five copies of a questionnaire to 1,991 households and received responses from 1,927 individuals (907 men, 1,008 women, 12 respondents of unspecified sex) in 1,029 households (51.7%). We estimated odds ratios (ORs) and 95% confidence intervals (CIs) for associations between high (vs. low) social capital and PTSD or other outcomes. After covariate adjustment, the odds of having PTSD were lower in participants with high cognitive social capital than those with low cognitive social capital (OR=0.346, 95%CI: 0.263-0.456). Elderly women with higher structural social capital tended to have lower PTSD odds than those with lower structural social capital (OR=0.671, 95%CI: 0.431-1.046). The opposite pattern was observed for elderly men (OR=1.315, 95%CI: 0.792-2.183). Cognitive social capital is a protective factor that may reduce PTSD or promote a favorable PTSD prognosis after heavy rainfall and flood events. The associations between structural social capital and PTSD differ by age and sex.