Background Enterococci are becoming the most important public health concern and emerging as multidrug-resistant organisms around the world including Africa particularly in Ethiopia where there is a lack of availability of effective antimicrobial drugs. However, there is a paucity of data on the prevalence and associated risk factors of vancomycin-resistant enterococci in Ethiopia. Objective This study was aimed to assess the prevalence of vancomycin-resistant enterococci and its associated risk factors among HIV-positive and -negative clients. Methods A comparative cross-sectional study was conducted from February to May, 2017, on 300 participants at Dessie Referral Hospital. Data were gathered using a pretested structured questionnaire, stool samples were collected and inoculated on to bile esculin agar, and presumptive colonies were inoculated in brain-heart infusion broth containing 6.5% NaCl for selective identification of enterococci. Antibiotic susceptibility tests were done using the Kirby–Bauer disk diffusion method. Data were analyzed using SPSS version 22 software package. Results A total of 300 study participants were enrolled in this study, of which 57.7% were females with a mean age of 34.4, a range of 19–73 years. The overall prevalence of enterococci was 37.3%. The prevalence of VRE was 6.3%. From all isolates, the prevalence of VRE among HIV-positive and -negative clients was 5.9% and 7.4%, respectively. Resistance gentamicin, ampicillin, penicillin, and erythromycin was 37.5%, 34.8%, 34.8%, and 22.3%, respectively. Prevalence of multidrug resistance was (29.5%). Being low in hemoglobin content was significantly associated with VRE. Conclusion The high prevalence of VRE and multidrug-resistant enterococci in this study signals the emergence of VRE. Detection of VRE in this study indicates decreased antibiotic treatment options of multidrug-resistant enterococci. Therefore, there should be a need to perform continuous surveillance, rational use of antibiotics, and more detailed study using phenotypic and genotypic methods.