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Background To achieve well-regulated distribution, storage, and utilization of rabies vaccine, health facilities should adhere to standard operating procedures. In Namibia, information on inventory management, utilization, monitoring and reporting of rabies vaccine adherence to standard operating procedures in public healthcare facilities is insufficient. The aim of this study was to assess adherence to rabies vaccine standard operating procedures and inventory management and, to compare rabies vaccine expenditure to the number of patients who received rabies vaccination at the Ministry of Health and Social Services public healthcare facilities from 2018–2020. Methods A cross-sectional, web-based questionnaire which consisted of closed-ended questions was sent to 147 pharmacy staff and warehouse managers working in the 14 regions of Namibia during the period of May 1, 2021 to June 2, 2021. The overall expenditure and the total number of patients vaccinated from 2018 to 2020 were obtained from national-level logistic and vaccination program coordinators. Data was coded and transcribed into Microsoft® Excel® 2013 and analysed using SPSS® version 27. Results One-hundred and thirty-three completed questionnaires were received from sixty-nine public health centres and hospitals. The group of respondents consisted of pharmacist assistants (50%), pharmacy technicians (12%), pharmacists (36.8%), senior pharmacists (0.8%) and chief pharmacists (1.5%). Overall, adherence to standard operating procedures was poor (27.1%). Rabies vaccine distributed to public health facilities from 2018 to 2020 was worth N$75,381,419.91 and was expected to vaccinate 87,269 patients, however, only 95 cases of both rabies cases and rabid dog-bite patients were reported. The major inventory management challenges for public healthcare facilities include inadequate number of pharmacy staff, poor adherence to standardized pharmaceutical warehousing, lack of regular supervision, and inadequate staff training. Conclusion Inventory management practices in public healthcare facilities were not in compliance with standard operating procedures. There is a significant discrepancy between rabies vaccine expenditure and the number of patients that were vaccinated. Therefore there is a need for adequate staff training on inventory management and regular facility supervision to enforce optimal rabies vaccine inventory management practices.