One of the issues that has engaged the human mind all the time is the difference created among human beings in terms of gender. The study was focused on the management performance of Higher Education Institution Academic Deans in the province of Bohol. Specially, the study ascertained the following: management performance academic deans as perceived by faculty members and academic deans, the difference on management performance between male and female academic deans as perceived by faculty members and academic deans and the difference on the perception of the faculty members and academic deans on the management performance of male and female academic deans. The study was conducted in the fourteen (14) HEI’s in the province of Bohol. The respondents were the 346 faculty members and 67 academic deans. The main instrument of this study was a modified survey questionnaire which underwent the process of validation so that reliable data can be deduced from the respondents. It contained the four-fold mandate of HEIs such as Instruction, Research, Extension, Production and also included Physical Facilities. The findings revealed that there was a difference with management performance of academic deans and perception of academic deans on the management capabilities male and female academic deans differ from the faculty members. This study concludes that it does not necessarily follow that male are better managers than female, both could comparably manage a school system. Further it is recommended that academic deans should be reoriented on their managerial roles of gender advocacy, sensitivity related activities must be encouraged, and seminars and in service training on management performance are to be held.