A devastating earthquake causes psychological distress, and may increase suicide mortality thereafter, yet previous studies have made inconsistent conclusions regarding this issue. The purpose of the present study was to determine whether the 2004 Niigata-Chuetsu earthquake in Japan affected long-term mortality from suicide. We conducted a comparative study of suicide mortality rates during the 5-year period preceding and the 3-year period following the earthquake in the disaster area and a control area in Niigata Prefecture, by analyzing death certificate data from October 1, 1999, to September 30, 2007. In men, baseline suicide mortality rates (5 years preceding the earthquake) were 48.4 per 100,000 person-years in the disaster area and 46.1 in the control area, and suicide mortality rates during the 3-year period following the earthquake were 46.0 and 45.1, respectively. In women, baseline suicide mortality rates were 22.3 in the disaster area and 18.7 in the control area, and post-earthquake suicide mortality rates were 20.2 and 15.3, respectively. In consequence, the decrease in suicide mortality rate during the 3 years post-earthquake was significantly higher in the disaster area (2.5) than in the control area (1.0) (p = 0.0013) in men, whereas the decrease in suicide mortality rate was 2.1 in the disaster area and 3.0 in the control area (p = 0.1246) in women. We have concluded that the long-term mortality from suicide after the earthquake decreases in men and increases in women, suggesting that post-earthquake suicide mortality is sex-dependent. Post-earthquake suicide prevention strategies should more aggressively target women.