Nigeria launched a ‘hub and spoke’ decentralization pilot in March 2010 for the provision of anti-retroviral therapy (ART). In this programme, stable ART patients at hospitals (hubs) were referred to primary health care centres (spokes) for the continued provision of ART. The objectives of this study are to compare the cost of ART care provided through the two levels of care. We also assess if decentralization was associated with changes in patients’ service utilization. Data were collected from facilities and patient records from Kaduna and Cross Rivers States. Costs were collected from the provider perspective. In Cross River, 398 patients and 528 from Kaduna were included in the retrospective cohort. The analysis utilizes separate fixed effect regressions for each state to assess differences in costs and service utilization among patients that decentralized. Uptake of decentralized services was ∼3% in Cross Rivers and ∼9% in Kaduna among active ART patients in April 2011. Patients electing to decentralize had 40% (95% CI: 13% to 67%) higher costs in Cross Rivers and 29% (−44% to −14%) lower costs in Kaduna as compared with patients that did not decentralize. Lower costs in Kaduna appear to result from shifting care to less expensive cadres of health workers (task shifting) rather than decentralization. Decentralization of health services is a complicated process and broad generalizations across settings and processes, concerning whether or not it reduces unit costs, are likely over-simplifications. Similarly, decentralization of ART services does not automatically increase access to ART care, and may limit access to ART laboratory services. This study is limited by not including costs incurred above the facility level, such as training, or costs borne by patients.