Until 2010, Burkina Faso was an exception to the international trend of abolishing user fees for antiretroviral treatment (ART). Patients were still expected to pay 1,500F CFA (2 Euros) per month for ART. Nevertheless, many non-governmental organizations (NGOs) exempted patients from payment. The objective of this study was to investigate how NGOs selected the beneficiaries of payment exemptions for government-provided ART and rationed out complementary medical and psychosocial services.For this qualitative study, we conducted 13 individual interviews and three focus group discussions (n = 13 persons) with program staff in nine NGOs (4,000 patients), two NGO coordinating structures and one national program. These encounters were recorded and transcribed, and their content was thematically analyzed. The results were presented to the NGOs for feedback.Results indicate that there are no concrete guidelines for identifying patients warranting payment exemptions. Formerly, ART was scarce in Burkina Faso and the primary criterion for treatment selection was clinical. Our results suggest that this scarcity, mediated by an approach we call sociotherapeutic rationality (i.e. maximization of clinical success), may have led to inequities in the provision of free ART. This approach may be detrimental to assuring equity since the most impoverished lack resources to pay for services that maximize clinical success (e.g. viral load) that would increase their chances of being selected for treatment. However, once selected into treatment, attempts were made to ration-out complementary services more equitably.This study demonstrates the risks entailed by medication scarcity, which presents NGOs and health professionals with impossible choices that run counter to the philosophy of equity in access to treatment. Amid growing concerns of an international funding retreat for ART, it is important to learn from the past in order to better manage the potentially inequitable consequences of ART scarcity.