We investigated the prognostic performance of scoring systems by the intensive care unit (ICU) type. This was a retrospective observational study using data from the Marketplace for Medical Information in the Intensive Care IV database. The primary outcome was in-hospital mortality. We obtained Sequential Organ Failure Assessment (SOFA), Acute Physiology and Chronic Health Evaluation (APACHE) III, and Simplified Acute Physiology Score (SAPS) II scores in each ICU type. Prognostic performance was evaluated with the area under the receiver operating characteristic curve (AUROC) and was compared among ICU types. A total of 29,618 patients were analyzed, and the in-hospital mortality was 12.4%. The overall prognostic performance of APACHE III was significantly higher than those of SOFA and SAPS II (0.807, [95% confidence interval, 0.799–0.814], 0.785 [0.773–0.797], and 0.795 [0.787–0.811], respectively). The prognostic performance of SOFA, APACHE III, and SAPS II scores was significantly different between ICU types. The AUROC ranges of SOFA, APACHE III, and SAPS II were 0.723–0.826, 0.728–0.860, and 0.759–0.819, respectively. The neurosurgical and surgical ICUs had lower prognostic performance than other ICU types. The prognostic performance of scoring systems in patients with suspected infection is significantly different according to ICU type. APACHE III systems have the highest prediction performance. ICU type may be a significant factor in the prognostication.