Purpose: To evaluate the performance and outcomes of the 6-minute magnetic resonance imaging (MRI) protocol in diagnosing stroke within Indonesian healthcare setting compared to computed tomography (CT). Patients and methods: This retrospective single-center study was conducted at the Universitas Indonesia Hospital in Depok, Indonesia from September 2021 to September 2023. Patients who were diagnosed with acute stroke underwent a clinical evaluation and a 6-minute MRI protocol. The primary objective was to assess the efficiency of the 6-minute MRI protocol in promptly and accurately evaluating acute stroke patients, including determining average MRI time, thrombolysis eligibility, and post-thrombolysis outcomes compared to CT imaging. Exclusions comprised those requiring resuscitation, lack of stroke code activation, or having incomplete documentation. Results: This study involved 182 stroke patients, 136 of which underwent MRI and 46 had CT scans. Thrombolysis eligibility was similar between the groups (48.9% for MRI vs 47.8% for CT-Scan), but a higher proportion of eligible MRI patients received thrombolysis (70.1% vs 54.5%, p = 0.037). MRI also achieved shorter door-to-imaging times, especially from February to June 2022. Among those treated for ischemic stroke via MRI, 70.3% showed improvement compared to 55% for CT (p=0.016). Door-to-MRI times varied across periods, averaging 88.2 minutes before national healthcare insurance collaboration, 29.1 minutes during transition, and 47.8 minutes afterward. Conclusion: This study emphasizes the crucial role of the 6-minute MRI protocol for accurately diagnosing stroke types, severity, and determining thrombolysis eligibility. Positive outcomes in thrombolysis patients using this protocol highlight its effectiveness. However, prolonged time-to-MRI indicates the need for further improvement. Optimizing time management and workflow efficiency are critical for improving treatment efficacy and safety. © 2025 Hidayat et al.