Introduction: Information on stroke mortality in people residing at high altitudes is controversial, and during the coronavirus disease 2019 (COVID-19) pandemic, there was a decrease in in-person care. Our objective is to evaluate mortality and functional prognosis after 3 months in stroke patients residing at high altitude during the COVID-19 pandemic. Methods: An analytical longitudinal study was conducted from January 2020 to January 2022 in a hospital in Cusco (3300 m above sea level), including adult patients diagnosed with stroke but without COVID-19 diagnosis, who were followed up for 90 days, evaluating mortality and functional disability (modified Rankin scale ≥ 3). Clinical and laboratory risk factors were evaluated, obtaining crude and adjusted hazard ratios (HR) through Cox regression models with 95% confidence intervals (CI95%). Results: One hundred twenty-three stroke patients were evaluated. After 90 days of follow-up, 28 patients (22.7%) died and 80 patients (65.0%) were diagnosed with functional disability. In models adjusted for gender, age, Alberta stroke program early CT (ASPECTS) score, and hypertension background, the only variable with increased risk was National Institutes of Health Stroke Scale (NIHSS) score at admission, both for mortality (HR 1.14, CI95% 1.09–1.20) and functional disability (HR 1.07, CI95% 1.04–1.11). Conclusions: Regarding stroke patients cared for in a high-altitude city during the COVID-19 pandemic, NIHSS score at admission is the most important risk factor for determining the 90-day mortality or functional disability, with a risk increase of approximately 10% for both outcomes for each additional point on the scale.

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