Background: Conventional laparoscopic cholecystectomy (CLC) is regarded as the gold standard for cholecystectomy. However, single-incision laparoscopic cholecystectomy (SLC) has been suggested to replace CLC. This study aimed at comparing long-term incidences of port-site hernia and chronic pain after SLC versus CLC. Methods: We conducted a matched cohort study based on prospective data (Jan 1, 2009–June 1, 2011) from the Danish Cholecystectomy Database with perioperative information and clinical follow-up. Consecutive patients undergoing elective SLC during the study period were included and matched 1:2 with patients subjected to CLC using pre-defined criteria. Follow-up data were obtained from the Danish National Patient Registry, mailed patient questionnaires, and clinical examination. A port-site hernia was defined as a repair for a port-site hernia or clinical hernia located at one or more port sites. Results: In total, 699 patients were eligible and 147 patients were excluded from the analysis due to pre-defined criteria. The rate of returned questionnaires was 83%. Thus, 552 (SLC, n = 185; CLC, n = 367) patients were analyzed. The median observation time was 48 months (range 1–65) after SLC and 48 months (1–64) after CLC (P = 0.940). The total cumulated port-site hernia rate was 4 % and 6 % for SLC and CLC, respectively (P = 0.560). Incidences of moderate/severe chronic pain were 4 % and 5 % after SLC and CLC, respectively (P = 0.661). Conclusions: We found no difference in long-term incidence of port-site hernia or chronic pain after SLC versus CLC.