Gender differences in treatment outcomes of 305 persons living with HIV receiving antiretroviral treatment (ART) in Kabarole district, western Uganda, were evaluated. The primary treatment outcome was virological suppression defined as HIV-1 RNA viral load (VL) <400 copies/ml and the secondary outcome measure was the increase in the CD4 cell count after six months on ART. Statistical analysis included descriptive, univariate, and multivariate methods. Proportionally, more females chose to seek treatment compared to males. After six months of treatment, females were more likely to have viral suppression (VL > 400 copies/ml) as compared to males (odds ratio 2.14, 95% confidence interval 0.99-4.63, p=0.05). While females had a significantly higher baseline CD4 cell count at initiation of treatment compared to males, the increase in CD4 cell count after six months on ART was similar in males and females. The reasons for better ART outcomes for females should be further investigated. Ideally, ART programs should work toward equitable treatment outcomes for men and women, if the cause of the gender differential lies in patient behavior and the way ART services are delivered.