The Bureau of Animal Industry was organized on January 31, 1930 pursuant to Act No. 3639 dividing the Bureau of Agriculture into two distinct entities: The Bureau of Plant Industry and the Bureau of Animal Industry.

Since its creation, the bureau went through several organizational changes, In 1932, Act No. 4007, known as the Reorganization Act of 1932, recognized the Bureau into 5 major entities: Office of the Director, Animal Husbandry Division, Animal Disease Control Division, Veterinary Research Division and Animal Product Division.

Under Commonwealth Act No. 340, approved by Congress on June 21, 1938, a fifth division entitled Animal Utilization Division was created.

On December 31, 1939, the Veterinary Research Division was abolished by Executive Order No. 240. In its stead, the Division of Parasitology and Protozoology and the Division of Pathology and Bacteriology were created.

In 1947, the Bureau again was subjected to another revamp. Under Executive No. 94 0f 1947, the Division of Parasitology and Protozoology and the Division of Pathology and Bacteriology were integrated to form the Veterinary Research Division. In 1953, two divisions were added to the expanding bureau, increasing the divisions to seven.

On January 6, 1957, by virtue of Reorganization Plan No. 30 as implemented by Executive Order No. 216, the bureau was subjected to a thorough reorganization. Bureau functions were realigned. Old Divisions retained were revitalized and new divisions were created to meet the ever widening responsibilities of the bureau.

The Veterinary Research Division, the Parasitic Diseases Division, the Animal Product Division and the Poultry Division were abolished. These divisions were created: the Animal Diseases and Parasitic Research Division to undertake all researches in animal diseases and parasites; the Laboratory Services Division to handle laboratory services and the manufacture of veterinary drugs and biologics; the Livestock and Poultry Propagation Division to undertake all the functions of former Animal Husbandry Division, excepts researches; the Livestock Research Division to conduct researches on nutrition, breed improvement, and management of poultry. An Office of the Director was constituted and the position of Assistant Director therein created.

The Administrative Division was renamed Administrative Services Division; the Animal Control Division, the Regulations and Control Division' and the Animal Husbandry Division, the Livestock and Poultry Propagation Division.

Through the years, the bureau underwent several more changes. It has expanded to seven Technical Divisions, namely: the Animal Health Division (formerly the Regulations and Control Division), the Animal Feeds Standard Division (formerly the Animal Feed Control Division), the Dairy Development Division, the Livestock Development Division (formerly the Livestock and Poultry Propagation Division), the Laboratory Services Division, the Marketing Development Division, and the Research Division.

The Philippine Animal Health Center and the Animal Products Development Center which were once UNDP's FAO assisted projects are now GOP regular projects of BAI. A third project, Farm Integrated Animal Health and Production Center (FIAHPC) maintains its foreign assistance from German Agency for Technical Cooperation. The function of the Dairy Development Division was recently absorbed by the newly established National Dairy Authority in 1997. Because of this transfer, today BAI has six divisions: Animal Feeds Standard, Animal Health, Laboratory Services, Livestock Development, Marketing Development and Research Development Division. With the enactment of Republic Act 8485 Animal Welfare Act of 1998, the bureau now have the Animal Welfare Division.