Background: The influence of atrial fibrillation (AF) and diabetes mellitus (DM) on early functional recovery in stroke survivors remains unclear. This prospective observational study investigated functional outcomes in stroke patients with AF and DM after early rehabilitation. Methods: Forty-six stroke patients (Mage = 70.1 ± 12.1, 50% female) who underwent early rehabilitation, were divided into AF/DM and non-AF/DM groups. Subsequently, a case-control sample was formed, matching patients by age and sex. Assessments at baseline and post-rehabilitation included the National Institutes of Health Stroke Scale, modified Rankin Scale, Rivermead Mobility Index, Barre Test, and simulator scores. Early rehabilitation consisted of individual therapeutic exercises initiated within the first 24 h post-stroke and simulator training (Thera Vital, Armeo Spring, Alter Step) which started 3–5 days later; the rehabilitation lasted 3.5 weeks (120 min 5 days per week). Results: Approximately 80% of the whole sample showed improvements, with no significant differences in recovery rates between groups. Age was identified as the only significantly different characteristic between improved and unimproved patients. Case-control analysis confirmed that AF and DM did not significantly influence early recovery. Discussion: These findings support the efficacy of early rehabilitation regardless of AF or DM status and emphasize the importance of timely intervention in stroke care. Given the limited sample size, further research with larger cohorts is necessary to validate these results and clarify the long-term effects of these comorbidities on stroke recovery. © The Author(s), under exclusive licence to Springer Nature Switzerland AG 2025.