Background: There is limited information on long-term outcomes after stroke in sub-Saharan Africa (SSA). Current estimates of case fatality rate (CFR) in SSA are based on small sample sizes with varying study design and report heterogeneous results. Aims: We report CFR and functional outcomes from a large, prospective, longitudinal cohort of stroke patients in Sierra Leone and describe factors associated with mortality and functional outcome. Methods: A prospective longitudinal stroke register was established at both adult tertiary government hospitals in Freetown, Sierra Leone. It recruited all patients ⩾ 18 years with stroke, using the World Health Organization definition, from May 2019 until October 2021. To reduce selection bias onto the register, all investigations were paid by the funder and outreach conducted to raise awareness of the study. Sociodemographic data, National Institute of Health Stroke Scale (NIHSS), and Barthel Index (BI) were collected on all patients on admission, at 7 days, 90 days, 1 year, and 2 years post stroke. Cox proportional hazards models were constructed to identify factors associated with all-cause mortality. A binomial logistic regression model reports odds ratio (OR) for functional independence at 1 year. Results: A total of 986 patients with stroke were included, of which 857 (87%) received neuroimaging. Follow-up rate was 82% at 1 year, missing item data were <1% for most variables. Stroke cases were equally split by sex and mean age was 58.9 (SD: 14.0) years. About 625 (63%) were ischemic, 206 (21%) primary intracerebral hemorrhage, 25 (3%) subarachnoid hemorrhage, and 130 (13%) were of undetermined stroke type. Median NIHSS was 16 (9–24). CFR at 30 days, 90 days, 1 year, and 2 years was 37%, 44%, 49%, and 53%, respectively. Factors associated with increased fatality at any timepoint were male sex (hazard ratio (HR): 1.28 (1.05–1.56)), previous stroke (HR: 1.34 (1.04–1.71)), atrial fibrillation (HR: 1.58(1.06–2.34)), subarachnoid hemorrhage (HR: 2.31 (1.40–3.81)), undetermined stroke type (HR: 3.18 (2.44–4.14)), and in-hospital complications (HR: 1.65 (1.36–1.98)). About 93% of patients were completely independent prior to their stroke, declining to 19% at 1 year after stroke. Functional improvement was most likely to occur between 7 and 90 days post stroke with 35% patients improving, and 13% improving between 90 days to 1 year. Increasing age (OR: 0.97 (0.95–0.99)), previous stroke (OR: 0.50 (0.26–0.98)), NIHSS (OR: 0.89 (0.86–0.91)), undetermined stroke type (OR: 0.18 (0.05–0.62)), and ⩾1 in-hospital complication (OR: 0.52 (0.34–0.80)) were associated with lower OR of functional independence at 1 year. Hypertension (OR: 1.98 (1.14–3.44)) and being the primary breadwinner of the household (OR: 1.59 (1.01–2.49)) were associated with functional independence at 1 year. Conclusion: Stroke affected younger people and resulted in high rates of fatality and functional impairment relative to global averages. Key clinical priorities for reducing fatality include preventing stroke-related complications through evidence-based stroke care, improved detection and management of atrial fibrillation, and increasing coverage of secondary prevention. Further research into care pathways and interventions to encourage care seeking for less severe strokes should be prioritized, including reducing the cost barrier for stroke investigations and care.