Pharmaceuticals together with salaries consume 60-80% of the health budgets of most counties in Kenya, therefore improving performance of the pharmaceutical commodity supply chain is one of the key activities aimed at improving health systems in Kenya. An efficient supply chain system reduces wastage and ensures availability of and accessibility to essential medicines, namely the right product in the right quality, in the right condition, at the right place, at the right time and at the right cost (the six rights of logistics). The purpose of this study was to evaluate the pharmaceutical commodities supply chain management challenges that health care workers of Busia County encounter while delivering services to the population and use the information to suggest improvements on the pharmaceutical supply chain performance. The study objectives were a) to determine how effective the Logistics Management Information System in Busia county is in serving her population needs b) to determine if funds allocated for procurement of medicines are efficiently utilized and c) to determine whether the staff using the pharmaceutical Logistics Management Information System and others in the supply management system are well trained on supply chain management and are of the right number. The study sites for this research were five facilities in each of the seven sub-counties in Busia County, whereby a sub-county hospital, a high volume health centre, a high volume and a low volume dispensary as well as one faith-based dispensary were targeted for this study. Main areas of research were the health facility pharmacy department, the comprehensive care clinic pharmacy, the pharmacy and county stores respectively. Cross-sectional descriptive study design was used. Instruments used were structured questionnaires, always, better and control analysis and also vital, essential and non-essential analysis respectively. The main findings were that most of the facilities experienced long lead time and delays in delivery of essential supplies, funds for procurement of medicines were well utilized but facility staffing levels were inadequate. The recommendations from this study are that, a) the county government should employ and train more health workers to support pharmaceutical commodity supply chain management b) the County Government should adopt efficient and effective supply chain management system, the Logistics Management Information System, so as to minimize waste and inefficiencies of county procured pharmaceutical commodities.