Medication errors at transition of care remain a concerning issue. In recent times, the use of integrated electronic medication management systems (EMMS) has caused a reduction in medication errors, but its effectiveness in reducing medication deviations at transition of care has not been studied in hospital-wide settings in Australia. The aim of this study is to assess medication deviations, such as omissions and mismatches, pre-EMMS and post-EMMS implementation at transition of care across a hospital. In this study, patient records were reviewed retrospectively to identify medication deviations (medication omissions and medication mismatches) at admission and discharge from hospital. A total of 400 patient records were reviewed (200 patients in the pre-EMMS and 200 patients in the post-EMMS group). Out of 400 patients, 112 in the pre-EMMS group and 134 patients in post-EMMS group met the inclusion criteria and were included in the analysis. A total of 105 out of 246 patients (42.7%) had any medication deviations on their medications. In the pre-EMMS group, 59 out of 112 (52.7%) patients had any deviations on their medications compared to 46 out of 134 patients (34.3%) from the post-EMMS group (p = 0.004). The proportion of patients with medication omitted from inpatient orders was 36.6% in the pre-EMMS cohort vs. 22.4% in the post-EMMS cohort (p = 0.014). Additionally, the proportion of patients with mismatches in medications on the inpatient charts compared to their medication history was 4.5% in the pre-EMMS group compared to 0% in the post-EMMS group (p = 0.019). Similarly, the proportion of patients with medications omitted from their discharge summary was 23.2% in the pre-EMMS group vs. 12.7% in the post-EMMS group (p = 0.03). Our study demonstrates a reduction in medication deviations after the implementation of the EMMS in hospital settings.