BACKGROUND: Pharmacy aseptic services are essential for many critical hospital services as they provide sterile and controlled environments under which highly qualified staff prepares injectable medicines. Although quantitative studies on problems of aseptic medicine services have been previously documented, there is a paucity of data to explain the cause of those problems. OBJECTIVE: This study aimed to examine practical challenges experienced by pharmacists during aseptic medicine services. METHODS: This was a qualitative study conducted using semistructured interviews. The participants were pharmacists working in various inpatient clinical environments in Yogyakarta Province, Indonesia. Participants were purposefully recruited through maximum variation and snowball sampling. The interview guide was developed after comprehensive literature review and discussions with some experts related to concepts in aseptic medicine service. Data were collected from April to August 2023 and analyzed via reflexive thematic analysis using the NVivo software. RESULTS: A total of 19 pharmacists working in 12 hospitals (7 public and 5 private) across the 5 regions in Yogyakarta Province were interviewed. The challenges in aseptic services can be grouped into 5 themes (1) unreliable physical facilities and equipment are the problems that should be solved, (2) shortage of the quality and quantity of human resources hinder the optimum aseptic medicine services, (3) competence, responsible, and accountable aseptic dispensing services management are needed to counter issues related work delegation, supervision, coordination, and communication between health staff, (4) various problems of production systems are needed to be considered, and (5) there is lack of pharmacist involvement in board of directors in making policy regarding aseptic services. CONCLUSION: By addressing the 5 main themes of challenges to aseptic medicine services, institutional leadership can begin to improve the patient safety and hospital performance. Incorporating experienced pharmacists into the decision-making processes at the executive level is a strategy to address these challenges.