Abstract Background and aims Chronic obstructive pulmonary disease (COPD) is present in 13% of atrial fibrillation (AF) patients. In patients diagnosed with both AF and COPD, we aimed to assess overall mortality risk and its association with temporal sequence in AF and COPD diagnosis. Methods This nationwide study assessed all patients aged 18–85 years diagnosed with both COPD and AF between 1999 and 2018 in Denmark. Three groups were defined according to the temporal sequence of diagnosis: COPD diagnosed at least 6 months before AF (COPD-First), AF diagnosed at least 6 months before COPD (AF-First) and COPD, and AF diagnosed within a 6-months’ time frame (AF∼COPD). Results We included 62 806 patients (75.0 years; 56.5% males). After 5 years of follow-up, 31 494 (50.1%) died. Mortality was highest in the COPD-First group (COPD-First: 52.8%; AF-First: 46.0%; AF∼COPD 50.6%). In a multivariable Cox-regression model adjusted for age, sex, type 2 diabetes, history of acute myocardial infarction, hypertension, heart failure, dyslipidemia, cancer, chronic kidney disease, and stroke, the AF∼COPD group (HR 1.19, 95% CI 1.16–1.23; P < 0.001) and COPD-First group (HR 1.30, 95% CI 1.27–1.33; P < 0.001) had a higher risk of death compared with the AF-First group. A restricted cubic spline analysis showed that the earlier the COPD was diagnosed, the worse is the prognosis. Conclusion Patients with concomitant AF and COPD had a very poor prognosis and the temporal sequence in diagnosis was differentially associated with prognosis, where a COPD diagnosis preceding an AF diagnosis was accompanied with a higher mortality risk compared with a COPD diagnosis following an AF diagnosis.