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Background Medicine shortages are a complex global challenge affecting all countries. This includes South Africa where ongoing medicine shortages are a concern among public sector hospitals as South Africa strives for universal access to healthcare. The objectives of this research were to highlight challenges in the current pharmaceutical procurement process for public sector hospitals. Subsequently, suggest potential ways forward based on the findings as the authorities in South Africa seek to improve the procurement process. Method Qualitative in-depth interviews were conducted with 10 pharmacy managers in public sector hospitals in the Gauteng Province, South Africa. A thematic content analysis was performed, with transcripts coded by two of the authors. Coding was discussed until consensus was reached. Categories were developed and grouped into themes. Results The ‘Procurement process’ emerged from the data as the overarching theme, rooted in three main themes: (i) The buy-out process that was used to procure medicines from suppliers other than the contracted ones; (ii) Suppliers not performing thereby contributing to medicine shortages in the hospitals; and (iii) Challenges such as the inaccuracy of the electronic inventory management system used in the hospitals. Conclusions Effective management of contracts of suppliers by the Provincial Department of Health is crucial to ensure accessibility and availability of essential medicines to all citizens of South Africa. Ongoing monitoring and support for the future use of computerised inventory management systems is important to reduce medicine shortages, and this is being followed up.