All programs undertaken by BAPSA are implemented and administered under the leadership of the Executive Director, BAPSA who works under the guidance of the Executive Committee (EC). The EC takes decisions on important issues on the basis of organizational policy guidelines from time to time. The management unit of all the projects have their office located at BAPSA Headquarter and are operating under the direct supervision of the Executive Director.

The organization follows standard practices and have the following manuals and policies: Human Resource policy, Financial policy, Gender policy, Sexual Harassment policy, Anti-corruption policy, HIV/AIDS policy, Child Protection policy. To provide clinical services BAPSA follows the government approved Manuals (FP, IUD, Infection Prevention Manual, EPI policy) and also WHO guideline on Post Abortion care and other relevant manuals.

Following are the number of Employees of BAPSA as on July, 2023: