Background . Healthcare-associated infection is a major public health problem, in terms of mortality, morbidity, and costs. Majorities of the cause of these infections were preventable. Understanding the potential risk factors is important to reduce the impact of these avoidable infections. The study was aimed to identify factors associated with healthcare-associated infections among patients admitted at Hiwot Fana Specialized University Hospital, Harar, Eastern Ethiopia. Methods . A cross-sectional study was carried out among 433 patients over a period of five months at Hiwot Fana Specialized University Hospital. Sociodemographic and clinical data were obtained from a patient admitted for 48 hours and above in the four wards (surgical, medical, obstetrics/gynecology, and pediatrics) using a structured questionnaire. A multivariate logistic regression model was applied to identify predictors of healthcare-associated infections. A p value Results . Fifty-four (13.7%) patients had a history of a previous admission. The median length of hospital stay was 6.1 days. Forty-six (11.7%) participants reported comorbid conditions. Ninety-six (24.4%) participants underwent surgical procedures. The overall prevalence of healthcare-associated infection was 29 (7.4%, 95% CI: 5.2–10.6). Cigarette smoking (AOR: 5.18, 95% CI: 2.15–20.47), staying in the hospital for more than 4 days (AOR: 4.29, 95% CI: 2.31–6.15), and undergoing invasive procedures (AOR: 3.58, 95% CI: 1.11–7.52) increase the odds of acquiring healthcare-associated infections. Conclusion . The cumulative prevalence of healthcare-associated infections in this study was comparable with similar studies conducted in developing countries. Cigarette smoking, staying in the hospital for more than 4 days, and undergoing invasive procedures increase the odds of healthcare-associated infections. These factors should be considered in the infection prevention and control program of the hospital.