Abstract Background Severe accidental hypothermia (AH) is life threatening. Thus, prognostic prediction in AH is essential to rapidly initiate intensive care. Several studies on prognostic factors for AH are known, but none have been established. We clarified the prognostic ability of the Sequential Organ Failure Assessment (SOFA) score in comparison with previously reported prognostic factors among patients with AH. Methods The J-point registry database is a multi-institutional retrospective cohort study for AH in 12 Japanese emergency departments. From this registry, we enrolled patients who were treated at the intensive care unit (ICU) in various critical care medical centers. In-hospital mortality was the primary outcome. We investigated the discrimination ability of each candidate prognostic factor and the in-hospital mortality by applying the logistic regression models with areas under the receiver operating characteristic curve (AUROC) with 95% confidence interval (CI). Results Of the 572 patients with AH registered in the J-point registry, 220 were eligible for the analyses. The in-hospital mortality was 23.2%. The AUROC of the SOFA score (0.80; 95% CI: 0.72–0.86) was the highest among all factors. The other factors were serum potassium (0.65; 95% CI: 0.55–0.73), lactate (0.67; 95% CI: 0.57–0.75), quick SOFA (qSOFA) (0.55; 95% CI: 0.46–0.65), systemic inflammatory response syndrome (SIRS) (0.60; 95% CI: 0.50–0.69), and 5A severity scale (0.77; 95% CI: 0.68–0.84). Discussion Although serum potassium and lactate had relatively good discrimination ability as mortality predictors, the SOFA score had slightly better discrimination ability. The reason is that lactate and serum potassium were mainly reflected by the hemodynamic state; conversely, the SOFA score is a comprehensive score of organ failure, basing on six different scores from the respiratory, cardiovascular, hepatic, coagulation, renal, and neurological systems. Meanwhile, the qSOFA and SIRS scores underestimated the severity, with low discrimination abilities for mortality. Conclusions The SOFA score demonstrated better discrimination ability as a mortality predictor among all known prognostic factors in patients with AH.