Background: The preventive effect of prophylactic amiodarone on postoperative atrial fibrillation (POAF) in patients undergoing thoracic surgery has previously been demonstrated. Meanwhile, the long-term effect remains unknown. We investigated the long-term effect of prophylactic amiodarone, in patients undergoing surgery for lung cancer, along with the long-term prognosis of patients with POAF within 6 years of follow-up. Methods: Using data from national databases, we retrospectively analysed 250 patients included and randomized, in the randomized control trial, PASCART, in which patients were allocated to receive either amiodarone or placebo as prophylaxis for POAF. Prophylactic groups, and subgroups, were compared on a number of outcomes. Long-term overall survival was evaluated using Kaplan-Meier survival curves, and Cox proportional hazards models were used for multivariable analysis. Competing risk analysis was used to evaluate time-to-event data in presence of competing risk. Results: When comparing the prophylactic groups, prophylaxis with amiodarone was not convincingly related to a higher frequency of long-term side effects. Patients who developed POAF, were more likely to develop late atrial fibrillation (AF) and POAF was associated with an increased risk of late AF in both the competing risk analysis hazard rate (HR) 4.80 [95% 1.75; 13.18] and multivariable analysis of the Cox regression, HR 5.03 [95% 1.80; 14.10]. When comparing the Kaplan Meier survival curves between groups, we found no statistically significant difference in the long-term overall survival. Conclusions: Intravenous prophylactic amiodarone is safe in patients undergoing lung cancer surgery. POAF is associated with an increased risk of late AF.