Access and availability of essential pharmaceutical services play significant role in ensuring betterrnhealth for the population. Implementation of integrated pharmaceutical logistics systems (IPLS)rnrequires use of LMIS forms and records. The study aims at assessing challenges in IPLSrnimplementation at ALERT hospital.rnThe study used eight research questions that are answered as a result the study. In this studyrndescriptive type of research was used with mixed method approaches where qualitative andrnquantitative data were collected in relation with challenges of implementing IPLS at hospital levelrnusing structured questionnaires and different secondary records and documents. The collected datarnwere analyzed using descriptive statistics and secondary documents and records were also reviewedrnand analyzed. Detailed results presented in this paper on key IPLS implementation indicators. Thisrnstudy assessed challenges about the availability and use of quality LMIS formats and records. Thernstudy explored barriers in human resources management including improving staff capacity, on howrnto complete the forms and records and use technology. This study assessed the challenges relatedrnwith infrastructure, finance, and application of regulatory policies and procedures in IPLSrnimplementation. The study looked in to challenges associated with stock availability and storagernconditions of pharmaceutical commodities and supplies at ALERT hospital. Human resources foundrnto be one of the critical challenge in the IPLS implementation that include shortage of staff, lack ofrntraining on pharmaceutical logistics, and there is no mechanism in place to address attrition andrnenhance motivation. More efforts and resources should be geared towards addressing financial,rninfrastructural and technology related challenges that affect IPLS implementation. ALERT hospitalrnstill using paper based LMIS and pharmaceutical logistics efforts are not yet linked with healthrninformation management system that captures and reports services data. More attention should berngiven to improve LIMS data use and its quality. It was also found that the management of thernhospital should address infrastructural issues around the store rooms including renovations andrnexpansion