Medication errors are a leading cause of preventable harm in hospitals. Electronic medication systems (EMS) have shown success in reducing the risk of prescribing errors, but considerable less evidence is available about whether these systems support a reduction in medication administration errors in paediatrics. Using a stepped wedge cluster randomized controlled trial we investigated changes in medication administration error rates following the introduction of an EMS in a paediatric referral hospital in Sydney, Australia. Direct observations of 284 nurses as they prepared and administered 4555 medication doses was undertaken and observational data compared against patient records to identify administration errors. We found no significant change in administration errors post EMS (adjusted Odds Ratio [aOR] 1.09; 95% CI 0.89-1.32) and no change in rates of potentially serious administration errors (aOR 1.18; 95%CI 0.9-1.56), or those resulting in actual harm (aOR 0.92; 95%CI 0.34-2.46). Errors in administration of medications by some routes increased post EMS. In the first 70 days of EMS use medication administration error rates were largely unchanged.