BackgroundThe importance of the health information system faces multiple challenges such as supply, acceptance, and pressure from other professions in Ethiopia. Work-related challenges might cause low professional satisfaction and hinder service provision. There is a paucity of evidence for policy decisions to improve these challenges. Therefore, this study aims to assess Health Informatics professional satisfaction in the Ethiopian health system and associated factors to provide evidence for future improvements.MethodsWe conducted an institutions-based cross-sectional study on health informatics professionals in three zones in Southern Ethiopia in 2020. We used a simple random sampling technique to select 215 participants. The local health officials were contacted regarding the research questions, and letters of permission were collected for data collection.ResultsOut of 211(98%) Health Informatics professionals who accepted the interview, 50.8% (95%CI: 47.74%-53.86%) were satisfied. Age (AOR = 0.57; 95% CI: 0.53, 0.95), experience (AOR = 5; 95% CI: 1.50, 19.30), working time (AOR = 1.35; 95% CI: 1.10, 1.70), working as HMIS officers (AOR 2.30; 95% CI: 3.80, 13), single marital status (AOR = 9.60; 95% CI: 2.88, 32), and urban residence (AOR = 8.10; 95% CI: 2.95, 22) were some of the associated factors.ConclusionsWe found low satisfaction among health informatics professionals compared to other studies. It was suggested that the responsible bodies must keep experienced professionals and reduce pressure from other professions through panel discussions. Work departments and working hours need consideration, as they are the determinants of satisfaction. Improving educational opportunities and career structure is the potential implication area.