There are three main bodies at the national level: the National Council, the National Executive Council and BPKS headquarters. These three bodies are based at the BPKS Complex in Dhaka .

The National Council is comprised of two members from each DPOD who are elected by their peers to represent the district Disabled Peoples' Organizations to Development (DPODs) at the national level. The BPKS Constitution requires that at least one representative from each DPOD is a woman. The National Council is the decision and policy making body for BPKS. It makes decisions about finances, future directions, activities and management of the organization.

There are currently 42 members of the National Council. The National Council at present comprises representatives of 28 district DPODs as well as representatives from other areas in Bangladesh . The BPKS Constitution allows people with disabilities who are working in the disability movement in areas without a DPOD to sit on the National Council for the temporary period.

Eleven members of the National Council are elected to the National Executive Council for a three year period. The National Executive Council ensures that the decisions of the General Council are implemented and decisions of the National Council are executed. [Members of the National Executive Council ]

BPKS Headquarters is the central body for policy coordination and the development of PSID programs at the national level. Different units work at BPKS Headquarters to provide support to the DPODs at district level. There is also an assistive devices production and service centre, an information and communication technology unit, a training and human resource development section and a job placement and advocacy unit. [ Locations ]

The Executive Director is the Chief Executive Officer of BPKS and ensures implementation of all programs and execution of all decisions made by the National Council and National Executive Council. He is responsible for the operations of all programs, fund raising and fund management. The Executive Director is also Member Secretary of the National Council and National Executive Council. The Executive Director is assisted by a Management Committee that is responsible for providing policy advice, reviewing budgets, recruitment, administration and ensuring appropriate implementations of programs.

It is a policy of BPKS that a minimum of 51% of all BPKS staff must be people with disabilities.