Summary Introduction Malnutrition is known as one of the major health problems among critically ill children; optimum nutrition support is considered as a therapeutic strategy to improve clinical outcomes and minimize the length of Pediatric Intensive Care Unit (PICU) staying as well as its costs. Implementation of an algorithmic protocol can result in the upgrade of the quality of nutrition support system in PICU. Method In this study, we developed a stepwise algorithmic nutrition care protocol for PICU patients in two phases as follows: a critical review of past literature and an expert discussion panel. The final structured protocol includes three following steps for the nutrition care process: 1) Initial nutrition screening and assessment, 2) Nutritional intervention and 3) Nutritional monitoring. Pre and post-implementation audits were carried out in a 23 bed medical/surgical PICU in a children's hospital affiliated to Mashhad University of Medical Sciences over two 4-week periods to evaluate the impact of the algorithm implementation. The post-implementation audit was performed by passing 12 weeks from the protocol implementation. Critically ill children aged between 1month and 10 years, and PICU length of stay>24 h who were in post gastrointestinal surgery state, were enrolled. Results Totally, 34 eligible critically ill gastrointestinal surgical children in post-implementation audit were compared with 30 patients with similar eligibility criteria in the pre-implementation audit. Notably, there were no significant differences in gender, median age, length of PICU stay, and mechanical ventilation requirement in the two audits. The comparison of our pre and post-implementation audits showed a significant increase in the proportion of energy delivery goal achievement following performing our intervention (56.7%, and 85.3%, for pre and post-implementation audits, respectively; p-value = 0.01).Additionally, time of achieving energy and protein goals were significantly decreased (5.5 vs. 3 days; p-value = 0.008 and 4 vs 3 days; p-value = 0.002, for energy and protein delivery goal achievements, respectively). Conclusion The implementation of the algorithm have significantly improved the adequacy ratio of energy delivery and also decreased the time to achieve the goal in energy and protein intake among critically ill children in post-gastrointestinal state. In this regard, further prospective studies are needed for continuing the evaluation of the algorithm implementation outcomes in critically ill children with different surgical and internal underlying diseases.