Background Treatment protocols and prices of antiretroviral therapy (ART) have changed over time. Yet limited data exist to evaluate the impact of these changes on patient outcomes and treatment costs in resource-poor settings. Methods We compared patient-level data on outcomes, utilization, and cost for the first two years of ART for a cohort of adult patients initiating ART in 2003–2004 and a cohort initiating ART in 2006–2008 at the GHESKIO clinic in Port-au-Prince, Haiti. Costs were measured from the health center perspective. Multivariate analyses were conducted to account for the potential impact of differences in disease severity at baseline. Results With the exclusion of patients who transferred care, 92% (167/181) of patients in the 2006–2008 cohort and 75% (150/200) in the 2003–2004 cohort were alive and in-care at the end of the study period. The mean cost per patient for the two-year study period was US$723 for the 2006–2008 cohort vs. US$1,191 for the 2003–2004 cohort, a cost difference of US$468 (p<0.0001). The mean cost per patient alive and in-care at the end of the two-year study period was US$744 for the 2006–2008 cohort vs. US$1,489 for the 2003–2004 cohort (p<0.0001). Conclusions HIV treatment outcomes in Haiti have improved over time while treatment costs declined by over 50% per patient alive and in-care at the end of the two-year study period. The major drivers in the reduction of treatment costs were the lower price of ART, lower costs for laboratory testing, and lower overhead costs.