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Background Delirium in critically ill children can result in long-term morbidity. Our main objectives were to evaluate the effectiveness of a new protocol on the reduction, prevalence, and duration of delirium and to identify associated risk factors. Methods The effectiveness of the protocol was evaluated by a chart review in all critically ill children aged 1 month to 15 years during the study period. A Cornell Assessment of Pediatric Delirium score ≥9 was considered positive for delirium. Data on delirium prevalence and duration from the pre-implementation and post-implementation phases were compared. Univariate and multivariate analyses were used to identify the risk factors of delirium. Results A total of 120 children was analyzed (58 children in the pre-implementation group and 62 children in the post-implementation group). Fifty children (41.7%) screened positive for delirium. Age less than 2 years, delayed development, use of mechanical ventilation, and pediatric intensive care unit (PICU) stay >7 days were significantly associated with delirium. The proportion of children screened positive was not significantly different after the implementation (before, 39.7% vs. after, 43.5%; P=0.713). Subgroup analyses revealed a significant reduction in the duration of delirium in children with admission diagnosis of cardiovascular problems and after cardiothoracic surgery. Conclusions The newly implemented protocol was able to reduce the duration of delirium in children with admission diagnosis of cardiovascular problems and after cardiothoracic surgery. More studies should be conducted to reduce delirium to prevent long-term morbidity after PICU discharge.