OBJECTIVE: To analyze the regional allocation of the resources from the Brazilian Popular Pharmacy Program, taking into account the relative availability of the program and the potential needs of the region. METHODS: Data from the National Health Survey of the Annual Report of Social Information and the administrative database of the program were used to create a non-parametric indicator of coverage using multiple data envelopment analysis technique. This indicator considers the relative availability of the program, taking into account equal access to equal needs (equity based on regional needs). The analysis of this indicator shows if the regions that most need pharmaceutical assistance are those that receive more resources from the Brazilian Popular Pharmacy Program. RESULTS: The states belonging to the richest regions of the country, Southeast and South, present wider relative coverage of the Brazilian Popular Pharmacy Program compared to poorer localities. In addition, the inequalities observed between locations are better explained by inefficiency in the transfer of resources to the basic component of pharmaceutical care than by the Brazilian Popular Pharmacy Program itself. According to the model, a 43.76% increase in the transfer to the basic component of pharmaceutical care would be required in order to improve equity, whereas the increase required by the Brazilian Popular Pharmacy Program is equivalent to 22.71%. CONCLUSIONS: Although the Brazilian Popular Pharmacy Program seeks to reduce the socioeconomic inequalities observed in access to pharmaceutical care, which integrates health care services, regional disparities in access to medicine persist. These regional differences are attributed mostly to allocation failures and problems in managing the conventional pharmaceutical care cycle provided through SUS pharmacies.