Background: Severity scores, including the Simplified Acute Physiology Score (SAPS) II, are widely used in the intensive care unit (ICU) to predict mortality outcomes using data from ICU admission or shortly hereafter. For patients with longer ICU length of stay (LOS), the predictive performance of admission-based severity scores may deteriorate compared to patients with shorter ICU LOS. This protocol and statistical analysis plan outlines a study that will assess the influence of ICU LOS on the performance of SAPS II for predicting 90-day post-ICU mortality. Methods: A Danish nationwide cohort study including adult (≥18 years) ICU patients admitted to a Danish ICU between 1 January 2012 and 30 June 2016. The study will be conducted using the Danish Intensive Care Database (DID), which contains data routinely, prospectively, and consecutively reported for all Danish ICU admissions. Discrimination of SAPS II for predicting 90-day post-ICU mortality will be assessed for the entire cohort and stratified according to ICU LOS. A first-level recalibration of SAPS II will be performed, and if adequate, standardised mortality ratios and calibration stratified according to ICU LOS will be reported. Conclusions: The outlined large, nationwide cohort study will provide important, contemporary information about the influence of ICU LOS on severity score performance relevant for ICU clinicians, researchers, and administrators. Publication of the protocol and statistical analysis plan prior to study conduct ensures transparency, and limits the risk of publication bias, post hoc changes in analyses, and challenges with multiple comparisons.