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Objectives Atrial fibrillation (AF) is the most common cardiac arrhythmia in the general population (GP). Patients with SLE may have an increased prevalence of AF due to chronic systemic inflammation. The aim of the study was to investigate the prevalence of AF in SLE cohort treated at the University Hospital (UH) of Split, in comparison with the GP of Split-Dalmatia County (SDC) and the Republic of Croatia (RC), and to analyze the association between AF with disease activity, organ involvement, and the use of oral anticoagulants (OAC).Methods 465 SLE patients were registered at UH Split from 1/2023 to 10/2025 of whom 20 patients had documented AF.We took the Croatian Institute for Public Health (CIPH) database reported sum of annual AF incidences (2017–2024) as an estimate of AF prevalence in the GP; denominator was the adult population in Croatia (RC= 3,204,957; SDC= 392,283). A two-tailed z-test for the difference in proportions and Fisher’s exact test were applied to assess associations between AF type and binary clinical features.Results The prevalence of AF in the SLE cohort was 4.3%, in the GP of Croatia 1.18% (z = 2.75; p = 0.006) and in GP of SDC 1.01% (z = 3.51; p < 0.001). Women accounted for 70% of SLE patients with AF, 3.4 times higher than in the Croatian GP AF population (20.4%) (z = 5.50; p < 0.001) and 3.9 times higher than in SDC (17.8%) (z = 6.08; p < 0.001). Persistent AF (perAF) was observed in 65% of patients, and paroxysmal AF (parAF) in 35%. Joint involvement was more frequent in parAF, while serositis was almost exclusively observed in perAF. OAC were used in 60% of patients, more often in perAF (p = 0.062).Conclusions The prevalence of AF in patients with SLE in SDC was significantly higher than in the GP of SDC and Croatia. PerAF was more often associated with serositis, while parAF was linked to joint involvement. The higher prevalence of AF in SLE may be partly explained by tight control in SLE, but the results indicate influence of chronic inflammation on the occurrence of AF.