Federally Qualified Health Centers (FQHCs) have long been important sources of care for publicly insured people living with HIV. FQHC users have historically used emergency departments (EDs) at a higher-than-average rate. This paper examines whether this greater use relates to access difficulties in FQHCs or to characteristics of FQHC users. Zero-inflated Poisson models were used to estimate how FQHC use related to the odds of being an ED user and annual number of ED visits, using claims data on 6,284 HIV-infected California Medicaid beneficiaries in 2008-2009. FQHC users averaged significantly greater numbers of annual ED visits than non-FQHC users and those with no outpatient usage (1.89, 1.59, and 1.70, respectively; P = 0.043). FQHC users had higher odds of being ED users (OR = 1.14; 95%CI 1.02-1.27). In multivariable analyses, FQHC clients had higher odds of ED usage controlling for demographic and service characteristics (OR = 1.15; 95%CI 1.02-1.30) but not when medical characteristics were included (OR = 1.08; 95%CI 0.95-1.24). Among ED users, FQHC use was not significantly associated with the number of ED visits in our models (rate ratio (RR) = 1.00; 95%CI 0.87-1.15). The overall difference in mean annual ED visits observed between FQHC and non-FQHC groups was reduced to insignificance (1.75; 95% CI 1.59-1.92 vs 1.70; 95%CI 1.54-1.85) after adjusting for demographic, service, and medical characteristics. Overall, FQHC users had higher ED utilization than non-FQHC users, but the disparity was largely driven by differences in underlying medical characteristics.