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Background: The pharmaceutical supply chain management system of Ethiopia has several problems including non-availability, poor storage, weak stock management and irrational use. However, few studies were conducted on progress and challenges towards implementation of Integrated Pharmaceuticals Logistics System (IPLS) in the study area. Therefore, this study aimed to assess the progress and challenges towards the implementation of IPLS in selected health facilities of Wollega zones, Western Ethiopia., Methods: A cross sectional quantitative and qualitative study was conducted in selected health facilities from February 15 to March 15, 2015. The calculated sample size was 31 health facilities with 20% margin of error and 90% confidence interval (CI). The Logistics Indicator Assessment Tool (LIAT) was used to collect information from selected health facilities; while an in-depth interview was held with chief pharmacist to collect qualitative data. Correlation and multiple linear regression analysis were used at significance level of 90%CI., Results: The average availability of bin cards for the selected products was 83.9% for hospitals, 75.4% for health centers, and 70.6% for health posts. On average, hospitals had an updated bin card for 43.8% of the product while health centers and health posts had an updated bin card for 32.9% and 32% of their products, respectively. On average the exact accuracy of request and resupply form (RRF) data for hospital and health center was 45.6% and 37.1%, respectively. IPLS implementation was related with health facility stores infrastructures (40.1%), Logistics Management Information System/LMIS/ (32.2%), stock availability and status (31.9%), storage condition (17.7%) and order fill rate (14.1%). Multivariable regression revealed LMIS (std. β = 2.539, p = 0.022), stock status (std. β = 0.848, p = 0.049) and availability of tracer medicines (std. β = 0.212, p = 0.013) were positively associated with IPLS implementation., Conclusion: There have been significant improvements in supply chain indicators in the availability of essential health commodities since IPLS has been implemented, with some variation by level of facility and product type. Involvement of all stakeholders is necessary to sustain the system. Additionally, there needs to be more focus on monitoring and evaluation of IPLS including more focused studies., (Copyright © 2020 Elsevier Inc. All rights reserved.)