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Objectives Accurate documentation of medication administration is crucial for patient safety. This study compares the accuracy of documentation between paper-based and electronic medication management (eMM) systems.Methods A secondary analysis of data from a stepped-wedge cluster randomised trial of an eMM implementation was conducted. The eMM module allowed electronic prescribing, recording of drug dispensing, drug administration and medication reconciliation and monitoring. Medication administration processes were observed in a tertiary paediatric hospital in Sydney, Australia. Trained nurse observers recorded details of medication administrations which were then compared with the information documented by nurses about the administrations.Results 5095 administrations were analysed. With eMM compared with paper, significantly fewer administrations had no time documented (adjusted OR (aOR) 0.15; 95% CI 0.07 to 0.34; p<0.001), but documented details were more often inaccurate (aOR 4.6; 95% CI 3.3 to 6.6). Fewer doses were administered from incorrect prescriptions with eMM (aOR 0.25; 95% CI 0.18 to 0.36).Conclusion eMM improves certain aspects of documentation but introduces new challenges, particularly in accurately recording administration details. Further investigation is needed to optimise these systems.Trial registration number Australian New Zealand Clinical Trials Registry 370325.