Gender disparity in healthcare sector leadership positions is a major problem among female healthcare professionals in Southern Ethiopia. This study explored gender disparities among healthcare professionals in healthcare sector leadership positions. The findings would be used to develop guidelines to reduce gender disparities in healthcare leadership in healthcare sectors to a minimum in Ethiopia. This study used exploratory and descriptive cross-sectional research design incorporating a mixed methods research approach to collect both quantitative and qualitative data simultaneously which were analyzed during the same phase of the research process. The quantitative survey data was collected using piloted structured questionnaire while qualitative data was collected using semi-structured interview guide containing open questions. Quantitative data was collected from a random sample of 414 healthcare professionals and qualitative data from a purposive sample of 21 healthcare professionals from seven districts having the experiences of gender disparity in healthcare leadership positions. Quantitative data had a compliance rate of 98% and it was entered into EpiData version 3.1 and exported to SPSS (version 24) for further analysis, and the qualitative data was coded and analyzed manually into thematic content. Quantitative findings of the study revealed that only 26% (n=108) of the participants reported that representation of women in healthcare sector leadership positions in the past few years has been increased. The majority of leadership positions assumed by study participants were at department head level while only 1.3 % were on chief excutive officers and 2.3% medical director positions respectively. Of these none was a female and 67%, n=264 of the participants do not have leadership role in a health service facility. Study participants having bachelor degree level of education were 2.3 times more likely to be represented in healthcare sector leadership positions than those participants having master’s degree and diploma [AOR=2.3, (95% CI: 1.289, 4.252)]. Challenges experienced by women health professionals regarding gender disparity in leadership positions in health service facility included family responsibilities, lack of support, lack of self-esteem or self-confidence, lack of career advancement, and cultural bias. The conclusions derived from the study was that women need all the opportunities, encouragement and support to allow them access to and success in healthcare sector leadership positions through informal and formal leadership training. / Health Studies / D. Litt et Phil (Health Studies)