Human immunodeficiency virus (HIV) and Helicobacter pylori (H. pylori) infections are worldwide healthcare burdens. This study aimed to assess the prevalence and associated factors of H. pylori infection among HIV patients at Southern-Ethiopia. A Hospital based cross-sectional study was conducted at Hawassa University comprehensive specialized hospital on 390 HIV infected adults on antiretroviral therapy from September to November 2017. All vital data were collected by designed questionnaires and stool samples were collected using appropriate sample cap for H. pylori stool antigen diagnosis. The overall prevalence of H. pylori infection of HIV infected patients was 17.9%. About 42.6% of the participants had a history of dyspepsia and of them, 4.3% were positive for H. pylori infection. In addition, 48.9% of patients were using either aqua tablet (67 mg-Trocloresene sodium) or water filters for drinking water, of them 11.5% were positive for H. pylori infection. Having a history of dyspepsia: the adjusted odds ratio [AOR (95% CI): 4.8 (1.6-14.7)], and age ≤30 years [AOR (95% CI):3.7(1.6-8.8)] were associated factors of H. pylori infection. Moreover, the association of H. pylori infection ≤ 30 years old and history of dyspepsia indicates the need of further large-scale and cohort type studies to determine the other possible associated factors for the infection.