There have been concerns about abuse and unnecessary chronic administration of zolpidem, and zolpidem's relation to suicide risk. To investigate the temporal association of zolpidem with the risk of suicide, we conducted a 12-year, population-based, retrospective cohort study on the National Health Insurance Service-National Sample Cohort (NHIS-NSC), South Korea. Data were collected from 2002 to 2013 from the NHIS-NSC, and data cleaning was performed for 1,125,691 subjects. Cox proportional hazards regression analysis was used to investigate the correlation over time between zolpidem medication and suicide. Over intervals commencing after 80 months of observation, the adjusted hazard ratio of suicides associated with the use of the zolpidem was 2.01 (95% CI: 1.58-2.56; p < 0.001). The mean cumulative number of days of zolpidem prescription was significantly longer in the suicide group than in the non-suicide group after log-transformation (p = 0.005). Cases of chronic use of zolpidem (over six months or one year) were significantly more common in the suicide group compared to the non-suicide group (p = 0.002 and 0.005, respectively). Subjects who received zolpidem medication had a significantly higher risk of suicide after at least 80 months of observation, suggesting a long-term increased suicide risk associated with insomnia exposed to zolpidem medication.