Atrial fibrillation (AF) is known to be a significant risk factor for poor prognosis after stroke. In this study, we compared differences in long-term outcomes after ischemic stroke among patients with AF and sinus rhythm (SR). We identified patients admitted to the reference Neurology Center between 1 January 2013 and 30 April 2015, inclusive, with acute ischemic stroke. Of the 1959 surviving patients, 892 were enrolled and followed for five years or until death. We analyzed the risk of stroke recurrence and death between patients with AF and SR at 1, 3, and 5 years after stroke. The rates of death and stroke recurrence were estimated using Kaplan–Meier analysis and multivariate Cox regression. During follow-up, 17.8% of patients died and 14.6% had recurrent stroke. The mortality in the AF group increased relative to the SR group with subsequent years. The risk of death was statistically higher in the AF than SR group at 1 year after stroke (13.5 vs. 7%, p = 0.004). After adjusting for age, stroke severity, and comorbidities, there was also no significant effect of AF on mortality in the first year after stroke (OR = 1.59, p = 0.247). There were no significant differences between the groups in stroke recurrence during follow-up. The results of our study showed that post-stroke patients with AF have a more severe prognosis, although AF itself does not have an independent negative effect on long-term outcomes after stroke. Long-term survival after stroke in patients with AF was strongly associated with age, stroke severity, and heart failure. The impact of other factors on prognosis after stroke in patients with AF should be considered.