This study aimed to define the problems of the current use of the e-Catalogue and the national formulary (NF)-two elements of medicine pricing and reimbursement policies in Indonesia for achieving universal health coverage (UHC)-by examining the knowledge and attitudes of stakeholders. Specifically, to investigate (1) the perceived challenges involved in the further implementation of the e-Catalogue and the NF, (2) reasons of prescribing medicines not listed in the NF, and (3) possible improvements in the acceptance and use of the e-Catalogue and the NF. Semi-structured interviews were conducted with stakeholders (policymakers, healthcare providers, a pharmaceutical industry representative, and experienced patients) to collect the qualitative data. The data was analysed using directed content analysis, following the guidelines of the COnsolidated criteria for REporting Qualitative studies (COREQ) in reporting the findings. Interestingly, 20 of 45 participants decided to withdraw from the interview due to their lack of knowledge of the e-Catalogue and the NF. All 25 stakeholders who fully participated in this research were in favor of the e-Catalogue and the NF. However, interviewees identified a range of challenges. A major challenge was the lack of harmonization between the lists of medicines in the e-Catalogue and the NF. Several system and personal reasons for prescribing medicines not listed in the NF were identified. Important reasons were a lack of incentives for physicians as well as a lack of transparent and evidence-based methods of selection for the medicines to be listed in the NF. The e-Catalogue and the NF have not been fully utilized for achieving UHC in Indonesia. Some possible improvements suggested were harmonization of medicines listed in the e-Catalogue and the NF, restructuring incentive programs for prescribing NF medicines, and increasing the transparency and evidence-based approach for selection of medicines listed in the e-Catalogue and the NF.