Background Antiretroviral therapy (ART) is used in human immunodeficiency virus (HIV) treatment to reduce morbidity and mortality rates among people living with the virus. The types of drug-related problems (DRPs) and their causes that contributed to HIV treatment failure were unknown. Thus, this study aimed to determine the types and causes of DRPs associated with HIV treatment failure. Methods A multicentre, retrospective cohort study was conducted at the Infectious Disease Centre of Sungai Buloh Hospital, Selangor, and Tuanku Ja'afar Hospital, Negeri Sembilan. Data were collected from patients' medical records by reviewing the medical progress notes, laboratory parameters, and treatment regimen. Pharmaceutical Care Network of Europe's (PCNE) classification system V9.1 was used to identify and classify the types and causes of DRPs. Patients were classified as having treatment failure if the HIV RNA viral load was more than 1000 copies/ml for two consecutive readings. Patients were categorized as treatment successful if there was a decrease in HIV RNA viral load suppression after six months of ART initiation and had no history of persistent HIV RNA viral load greater than 1000 copies/ml for two consecutive measurements. Data were analyzed using the chi-square test. Results The number of patients recruited for this study was 355 (treatment success group = 263, treatment failure group = 92). Almost all patients (n = 354, 99.7%) had experienced at least one DRP. A total of 811 problems and 1605 causes of DRPs were encountered. The occurrence of DRPs in the HIV treatment failure group was 5.77 DRPs per patient compared to the success group (4.08 DRPs per patient). In the treatment failure group, treatment effectiveness was identified as the most frequent domain of problems (P) (P1: n = 169, 59.93%), followed by treatment safety (P2: n = 111, 39.36%). The common domains of causes (C) include patient-related (C7: n = 367, 69.11%), other (C9: n = 105, 19.77%), and drug selection (C1: n = 49, 9.23%). Significant differences were found in several causes (C7.1, C7.10, and C9.1) between the two groups. Conclusion The occurrence of DRPs in HIV treatment failure was high, contributing to treatment effectiveness and treatment safety issues.