Background: Inadequate human resources are a major constraint to improving global health. The health sector is characterized by a high turnover coupled with internal as well as external brain drain but there is little information on intention to leave among health professionals in public health centers of Jimma Zone, Oromia Regional State. The aim of this study is to assess intention to leave and associated factors among health professionals in public health centers of Jimma Zone, southwest Ethiopia. Methods: A cross-sectional quantitative and qualitative study was conducted on seven randomly selected woredas (districts) which have 53 public health centers. All health professionals in sampled district public health centers were included (n = 505). Factor analysis was employed for all Likert scale instruments to extract factor(s) representing each of the scales using SPSS version 16.0. The qualitative data was analyzed by thematic analysis methods. Ethical approval was obtained from Jimma University. Results: Four hundred fifty five (90.1%) health professionals participated in the study; out of this, 290 (63.7%) had intention to leave. Among variables, job satisfaction (Beta = −0.298, (95% CI, −0.568 to −0.029), working environment (Beta = −0.612, (95% CI, −0.955 to −0.270), and organizational management (Beta = −0.552, (95% CI, 0.289 to 0.815) had statistically significant association with intention to leave among health professionals in public health centers of Jimma Zone. Conclusions: The overall intention to leave among health professionals was high. Level of job satisfaction, working environment, work pressure, and organizational management had statistically significant association with intention to leave. Thus, responsible bodies should aggressively work on the concerns identified, like, improvements in salary, promotion in terms of training/educational opportunity, improving working environment, and transfer of health professionals, and improvement of the leadership skills of managers.