PURPOSE: While patients with autoimmune diseases (ADs) are at high risk for developing specific malignancies, including lung cancer, ADs may protect against the development of cancer through increased immune cell activity in tumors. This study aimed to investigate whether the presence of ADs affects surgical outcomes and survival after surgery for lung cancer. METHODS: The medical records of 1236 patients who underwent surgery for non-small cell lung cancer between 2007 and 2018 were retrospectively reviewed. Perioperative and long-term outcomes were compared between patients with and without ADs using propensity score matching. RESULTS: Among the included patients, 115 with ADs and 1121 without ADs underwent surgery. Using 1-to-1 propensity score matching, 114 pairs were selected. Although there were no significant differences in the perioperative outcomes of the two groups, the overall and relapse-free survival rates were significantly lower in the group with ADs than in the group without ADs. CONCLUSIONS: Surgery for lung cancer can be performed without increasing the complications in patients with ADs. However, the long-term outcomes were significantly worse in patients with ADs than in those without ADs, suggesting that close follow-up for lung cancer and careful whole-body examination might be needed for patients with ADs.