Background: The new coronavirus disease (COVID-19), a pandemic infection caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2), had a deep global influence on morbidity and mortality profiles. Comorbidities, especially cardiovascular diseases, were identified to strongly modify the clinical course of COVID-19. However, the prognostic role of incident or prevalent atrial fibrillation has not been fully explained. The aim of this study was to evaluate the association between atrial fibrillation and outcomes following hospitalization in patients with severe COVID-19. Methods: We analyzed 199 patients (72 female, median age 70 years) with severe COVID-19 hospitalized between November 2020 and February 2021, due to SARS-CoV-2 infection. The study cohort included 68 patients with a history of AF (34 patients with paroxysmal AF, 19 with permanent AF, 15 patients with persistent AF), and 51 patients presented with AF during hospitalization. Results: Overall mortality during 90 days from the admission to hospital was 41% (n = 82). Non-survivors were older, had significantly elevated inflammation markers (CRP, WBC, procalcitonin, IL-6), NT-proBNP and D-dimer on the first day of hospitalization, lower left ventricular ejection fraction and worse kidney function, as compared to those who stayed alive during the follow-up. Among the hospitalized patients with COVID-19, a history of AF and the presence of AF during hospitalization contributed to higher mortality. Patients with permanent and persistent AF were at the highest risk of death. Different presentations of AF (any history of AF, the subtypes of AF—paroxysmal, permanent, persistent—and the presence of AF during hospitalization) were included in multivariate analysis, aiming to identify independent risk factors of death in the study period. We found that AF was related to worse prognosis, and persistent or permanent forms represented an independent predictor of mortality. Conclusions: Different clinical presentations of AF have varying impacts on survival in severe COVID-19. Mortality in hospitalized patients with severe COVID-19 was higher among patients with a history of AF, especially with persistent and permanent types of AF, and with AF present during hospitalization.