Introduction The National Oncology Institute of Morocco's (NIO) shift to an automated cytotoxic drug preparation system (PHARMODUCT®) has prompted an evaluation of its economic and clinical impacts compared to traditional manual methods. Methods A retrospective cost-benefit analysis over six months, extrapolated to annual projections, assessed initial investments, labour, equipment, drugs and consumables. Four commonly used chemotherapy drugs were analyzed, with a focus on the cost implications of drug waste in manual preparation versus the efficiency of vial-sharing in automated methods. Results The automated system incurred a higher initial cost $2,934,098.74, but reduced annual drug consumption costs by 19.74% and drug-related expenses by $41,228.27. It also decreased personnel costs by $48,073.35. Despite the upfront investment, the system is projected to break even within two years, with no medication waste due to its vial-sharing capability. Conclusion The initial higher investment in pharmaceutical automation promises considerable long-term savings and efficiency gains. Despite the study's limited scope and duration, the findings endorse the adoption of automated systems in oncology pharmacy settings for sustainable financial management and improved clinical outcomes.