The Brookhaven Site Office (BHSO) is an organization within the U.S. Department of Energy's Office of Science with responsibility to oversee and manage the Management and Operating (M&O) contract for the Brookhaven National Laboratory (BNL) in Upton, New York.

BNL is one of ten Office of Science Laboratories and is a multi-program laboratory with a primary mission on delivering breakthrough science and technology in the areas of Physics and chemistry materials, Environmental and Energy Research, and Structural Biology. BNL also performs work for the National Nuclear Security Administration (NNSA) and a host of other Federal agencies. The BHSO is responsible for program implementation, acquisition management, and laboratory stewardship at BNL. Through its oversight role, the BHSO is affecting the safe and efficient operation of BNL while enabling the pursuit of visionary research and development in support of DOE's missions.