Background and Objectives: Patients at high altitudes with COVID-19 may experience a decrease in their partial oxygen saturation (PO2S) levels. The objective was to assess the association between PO2S and intensive care unit (ICU) stay in patients at high altitudes with COVID-19. Materials and Methods: Clinical records of 69 COVID-19 patients (36% women) admitted to the ICU were analyzed. Median values were considered for intra-group categories (“≤11 days” and “>11 days” in the ICU) and for PO2S height categories (“<90%” and “≥90%”). Logistic regression and linear regression models adjusted for confounding variables were used. Results: Patients with >11 days in the ICU had 84% lower odds of having a PO2S ≥ 90% (OR: 0.16 [CI: 0.02, 0.69], p = 0.005) compared to those with ≤11 days in the ICU. An increase in PO2S by 1% reduced ICU stay by 0.22 days (β: −0.22 [CI: −0.33, −0.11], p < 0.001), potentially leading to a reduction of up to 1.44 days. Conclusions: PO2S is a crucial factor in estimating ICU stays for COVID-19 patients at high altitudes and serves as an accessible and cost-effective measure. It should be used in infected patients to complement the prognosis of post-pandemic ICU stay.