Perforated peptic ulcer (PPU) is a surgical emergency associated with high short-term mortality. However, studies on long-term outcomes are scarce. Our aim was to investigate long-term survival after surgery for PPU. A population-based, consecutive cohort of patients who underwent surgery for PPU between 2001 and 2014 was reviewed, and the long-term mortality was assessed. Survival was investigated by univariate analysis (log-rank test) and displayed using Kaplan-Meier survival curves. Multivariable analysis of risk factors for long-term mortality was assessed by Cox proportional hazards regression and reported as hazard ratio (HR) with 95 % confidence intervals (CI). A total of 234 patients were available for the calculation of ninety-day, one-year and two-year mortality, and the results showed rates of 19.2 % (45/234), 22.6 % (53/234) and 24.8 % (58/234), respectively. At the end of follow-up, a total of 109 of the 234 patients (46.6 %) had died. Excluding 37 (15.2 %) patients who died within 30 days of surgery, 197 patients had long-term follow-up (median 57 months, range 1-168) of which 36 % (71/197) died during the follow-up period. In multivariable analyses, age >60 years (HR 3.95, 95 % CI 1.81-8.65), active cancer (HR 3.49, 95 % CI 1.73-7.04), hypoalbuminemia (HR 1.65, 95 % CI 0.99-2.73), pulmonary disease (HR 2.06, 95 % CI 1.14-3.71), cardiovascular disease (HR 1.67, 95 % CI 1.01-2.79) and severe postoperative complications (HR 1.76, 95 % CI 1.07-2.89) during the initial stay for PPU were all independently associated with an increased risk of long-term mortality. Cause of long-term mortality was most frequently (18 of 71; 25 %) attributed to new onset sepsis and/or multiorgan failure. The long-term mortality after surgery for PPU is high. One in every three patients died during follow-up. Older age, comorbidity and severe postoperative complications were risk factors for long-term mortality.