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Abstract Background Patient safety is a central healthcare policy worldwide. Adverse drug events (ADE) are among the main threats to patient safety. Children are at a higher risk of ADE in each stage of medication management process. ADE rate is high in the administration stage, as the final stage of preventing medication errors in pediatrics and neonates. The most effective way to reduce ADE rate is using medication administration clinical decision support systems (MACDSSs). The present study reviewed the literature on MACDSS for neonates and pediatrics. It identified and classified the data elements that mapped onto the Fast Healthcare Interoperability Resources (FHIR) standard and the functionalities of these systems to guide future research. Methods PubMed/ MEDLINE, Embase, CINAHL, and ProQuest databases were searched from 1995 to June 31, 2021. Studies that addressed developing or applying medication administration software for neonates and pediatrics were included. Two authors reviewed the titles, abstracts, and full texts. The quality of eligible studies was assessed based on the level of evidence. The extracted data elements were mapped onto the FHIR standard. Results In the initial search, 4,856 papers were identified. After removing duplicates, 3,761 titles, and abstracts were screened. Finally, 56 full-text papers remained for evaluation. The full-text review of papers led to the retention of 10 papers which met the eligibility criteria. In addition, two papers from the reference lists were included. A total number of 12 papers were included for analysis. Six papers were categorized as high-level evidence. Only three papers evaluated their systems in a real environment. A variety of data elements and functionalities could be observed. Overall, 84 unique data elements were extracted from the included papers. The analysis of reported functionalities showed that 18 functionalities were implemented in these systems. Conclusion Identifying the data elements and functionalities as a roadmap by developers can significantly improve MACDSS performance. Though many CDSSs have been developed for different medication processes in neonates and pediatrics, few have actually evaluated MACDSSs in reality. Therefore, further research is needed on the application and evaluation of MACDSSs in the real environment. Protocol Registration (dx.doi.org/10.17504/protocols.io.bwbwpape).