All programs undertaken by BAPSA are implemented and administered by the director, BAPSA who works under the guidance of the Executive Committee. The EC takes decisions on important issues and formulate policy guidelines from time to time. The decisions of the Executive Committee are implemented by the Director, BAPSA while implementing the project. Accordingly the centers are managed by the guidance of the central office’s decisions and day to day operation is being carried out by the center’s managements. In case of critical issues the center inform the central management and central office provide decisions to solve the problems.

The organization follows standard practices and have the following manuals and policies: Recruitment policy( HR Manual),Procurement policy(Financial manual ),Gender policy, Sexual Harassment policy, Anticorruption policy, Financial Manual, Internal Control Policy /audit, HIV/AIDS policy, and Child Protection policy and for providing clinical services follow the government approved Manuals(FP,IUD, Infection Prevention Manual, EPI policy) and also WHO policy on providing Post Abortion care and other relevant manuals.