Using reliable evidence from routine health information system (RHIS) over time is a vital aid to improve health outcome, tackling disparities, enhancing efficiency, and encouraging innovation. In Ethiopia, utilization of routine health data for improving the performance and quality of care was not well-studied in grassroot health facilities. This study was conducted to determine the level of RHIS utilization and associated factors among health professionals in public health facilities of Dire Dawa, eastern Ethiopia. An institution-based cross-sectional study was conducted among 378 health professionals from June 10 to July 20, 2020. Self-administered pretested-structured questionnaire was used to collect data from the participants. Data were entered using EpiData 3.1 and analyzed using Stata 16.0. Descriptive statistics was used to describe the basic characteristics of the participants, and multivariable logistic regression analysis was conducted to identify factors associated with RHIS utilization. Adjusted odds ratio (AOR) (95% CI) was used to report association and significance declared at a P-value <0.05. Good RHIS utilization among health professionals was 57.7% (95% CI: 52.6%, 62.6%). Good organizational support (AOR = 3.91, 95% CI: 2.01, 7.61), low perceived complexity of RHIS formats (AOR = 2.20, 95% CI: 1.23, 3.97), good self-efficacy (AOR = 2.52, 95% CI: 1.25, 5.10), and good decision-making autonomy (AOR = 3.97, 95% CI: 2.12, 7.43) were important factors associated with good RHIS utilization. The level of good RHIS utilization among health professionals was low. Lack of self-confidence and empowerment, complexity of RHIS formats, and poor organizational support were significantly reducing RHIS utilization. Therefore, improving self-efficacy and decision-making capacity of health professionals through comprehensive training, empowerment, and organizational support would be essential.