Background Pharmaceutical’s procurement is a core component of logistics management, and has a significant influence on product availability, and total supply chain costs. In Ethiopia, there are few studies on this topic where almost all of them were from suppliers’ perspectives and entirely quantitative. This study, therefore, aimed to assess health professionals’ perceptions about pharmaceuticals procurement performance in public health facilities in southwest Ethiopia. Methods A facility-based cross-sectional study complemented with a qualitative method was conducted from March 20 and April 30, 2019. We collected the quantitative data through self-administered structured questionnaires from pharmacy staff and document review using checklists. EpiData version 3.1 and SPSS version 20 were used for data entry and analysis, respectively. Descriptive statistics were done for quantitative data. Qualitative data were gathered through face-to-face in-depth interviews and analyzed using thematic analysis technique. Results Regarding respondents’ perception of accountability in pharmaceutical procurement, 110 (57.9%) agreed or strongly agreed that their facilities adopt and use standard treatment guidelines and facility-specific medicine lists. Concerning competitiveness, 139 (62.6%) of the participants either disagreed or strongly disagreed that their facilities used formal suppliers’ qualifications based on service reliability and financial capacity. Regarding efficiency, 146 (76.8%) disagreed or strongly disagreed that their facilities develop a mechanism for prompt, reliable payment to lower medicine prices. The qualitative analysis identified staff workforce and competency, budget shortages, suppliers’ uncertainty, and pharmaceutical non-availability as challenges for procurement management performance. Conclusion The results indicated that participants perceived procurement performance of their facilities as poor. Therefore, staff development, fundraising options, monitoring and evaluation, coordination and collaboration can improve procurement practice and performance.