High quality of care (QoC) for antiretroviral treatment (ART) is essential to prevent treatment failure. Uganda, as many sub-Saharan African countries, increased access to ART by decentralizing provision to districts. However, little is known whether this rapid scale-up maintained high-quality clinical services. We assess the quality of ART in the Acholi and Lango sub-regions of northern Uganda to identify whether the technical quality of critical ART sub-system needs improvement. We conducted a randomized cross-sectional survey among health facilities (HF) in Acholi (n = 11) and Lango (n = 10). Applying lot quality assurance sampling principles with a rapid health facility assessment tool, we assessed ART services vis-à-vis national treatment guidelines using 37 indicators. We interviewed health workers (n = 21) using structured questionnaires, directly observed clinical consultations (n = 126) and assessed HF infrastructure, human resources, medical supplies and patient records in each health facility (n = 21). The district QoC performance standard was 80% of HF had to comply with each guideline. Neither sub-region complied with treatment guidelines. No HF displayed adequate: patient monitoring, physical examination, training, supervision and regular monitoring of patients’ immunology. The full range of first and second line antiretroviral (ARV) medication was not available in Acholi while Lango had sufficient stocks. Clinicians dispensed available ARVs without benefit of physical examination or immunological monitoring. Patients reported compliance with drug use (>80%). Patients’ knowledge of preventing HIV/AIDS transmission concentrated on condom use; otherwise it was poor. The poor ART QoC in northern Uganda raises major questions about ART quality although ARVs were dispensed. Poor clinical care renders patients’ reports of treatment compliance as insufficient evidence that it takes place. Further studies need to test patients’ immunological status and QoC in more regions of Uganda and elsewhere in sub-Saharan Africa to identify topical and geographical areas which are priorities for improving HIV care.