OBJECTIVES: Access to affordable quality essential medicines in developing countries like Nigeria continues to be a challenge despite interventions by relevant stakeholders. Inadequate management of the medicines supply chain is a major contributing factor. Hence, this study aims at identifying factors that may be militating against efficient supply chain management (SCM) of medicines in Nigeria METHODS: A mixed methods approach was used to obtain data from logistics companies and pharmacists in Nigeria. Structured questionnaires were administered to logistics companies while in-depth interviews were conducted for pharmacists purposively selected to capture a diverse range of experiences, practice areas and opinions. Quantitative and qualitative data were analyzed using descriptive statistics and thematic analysis respectively. RESULTS: Logistics companies are not adequately equipped and no monitoring is in place to ensure that standards are set and followed. 84% of logistics companies had no set of standard operating procedures for medicines logistics. 37% are capable of providing cold chain logistics depending on the duration. 47% had no temperature monitoring devices. There was no form of regulation enforcing standards for medicines logistics, with implications for treatment failure. Pharmacists’ views suggest that poor logistics and SCM practices, poor health statistics, weak regulation and policy implementation and lack of support for in-country medical logisticians are factors affecting efficient SCM of medicines. CONCLUSIONS: Factors militating against effective logistics and SCM of medicines were identified. Hence the need for establishing measures to improve the situation. Such measures may include more political will in implementing policies, financing SCM of medicines, building in-country skills and capacity in SCM of medicines, individualizing and segmenting medicines supply chains, and creating a regulatory body for certifying and professionalizing medical logistics companies, medical logisticians and supply chain managers in Nigeria, amongst others. These may lead to improved patient outcomes through better access to quality and affordable medicines