Background Zinc supplementation for diarrhea treatment is relatively easy to implement and inexpensive intervention that through numerous clinical trials has shown beneficial results in reducing the severity and duration of diarrheal episodes in children younger than five years of age. Adherence to prescribing and administration levels of zinc appear to be low in low to middle income countries. The prescribing practice of the health professionals and their adherence to the set protocol is also affected by many different factors. Objective The objective of this study is to measure zinc prescribing practice and factors affecting prescribing of zinc supplementation in management of childhood diarrhea among health professionals at Health facilities in Addis Ababa, Ethiopia. Methods Cross sectional study design was employed on 481 health professionals working in health facilities found in selected five sub cities in Addis Ababa to determine zinc prescribing practice. Quantitative data were collected using self-administered questionnaires. For the comprehensiveness of the study prescription paper review and facility observation was made to check availability of the product and other facility related factors. Data was entered using EpiData 3.1 and analyzed using SPSS version 20. Result A total of 481 prescribing health professionals participated in the study of which 17.9% had taken the IMNCI training. Prescribing of zinc as per the standard recommendation was found to be 45.2%.Among all the participants 58.4% were found having adequate knowledge and 55.1% do have a good attitude. In this study, Training, working in IMNCI and pediatrics departments, adequate knowledge and good program and facility perceptions were positively associated with zinc prescribing practice. In prescription paper review, zinc prescribing as per the standard recommendation was found from 24.9% of the prescriptions and facility observation has showed 71.9 % of the facilities have zinc stock at the time of visit. Conclusion The study has witnessed there is a gap in prescribing practice of zinc, overall knowledge associated with zinc and in its effective utilization for diarrhea management. Recommendation Efforts should be made to increase the knowledge level of the prescribing health professionals, trainings should be given on child case management and also regular sensitization should be in place. Nationally as child health program, better awareness creation is recommended about the effectiveness of zinc for diarrhea management, the untoward consequence of irrational antibiotic prescribing for diarrhea and also strive to ensure zinc availability at all time in the health facilities.