BACKGROUND: Primary healthcare (PHC) is essential for health systems worldwide, and resource allocation is vital for sustainability. However, various challenges hinder the allocation process, negatively affecting health outcomes. Therefore, this study explored the current challenges related to financial resource allocation within the PHC system in Iran. MATERIALS AND METHODS: This study is a qualitative descriptive study conducted on the basis of the guide provided by Villamin et al. Data were collected through semi-structured interviews. Accordingly, 20 interviewees were selected via a purposive and snowball sampling approach. The interviewees were experts in budgeting, primary healthcare, and health policies. This study was conducted in 2024. Data were collected between May 2024 and October 2024. The interviews continued until the saturation point was reached. The interview data were analysed via an inductive thematic analysis approach. MAXQDA version 2020 and Microsoft Excel were used for data extraction. RESULTS: The challenges associated with financial resource allocation were categorized into five main themes, eight subthemes, and 25 codes. Themes (subthemes) included the population base (demographic and geographical), health needs (epidemiological), governance (policymaking and political), implementation (process-related and management) and impact (financial). CONCLUSIONS: The findings provide a comprehensive set of challenges for allocating financial resources to PHC. Addressing these challenges is essential for health system managers, policymakers and political leaders. Additionally, awareness of PHC financial resource allocation challenges and how to address them clearly demands a multifaceted approach. Successful outcomes depend on collaboration amongst managers at the health system's macro, meso, and micro levels. Such cooperation will be instrumental in creating an effective allocation of financial resources that supports the ongoing development and sustainability of PHC initiatives.