The Bureau was part of a package of new agencies created to provide the impoverished United States territory with a state-like government.

During the incumbency of the longest-serving Director, Lou Montañez, the name of the agency was changed to Office of Budget and Management by Law 147 of 1980.

The name, as well as the emphasis of the agency's focus, was once again changed by Law 110 of 1995, when it was renamed Office of Management and Budget under executive director Jorge Aponte, who expanded the technological side of the agency and added to the director the role of becoming the government's Chief Information Officer or CIO.

In 2005, while Ileana Fas served as its director, the Office confronted the first time in Puerto Rico's history in which the new budget, approved by a New Progressive Party-dominated legislature presided by House Speaker José Aponte Hernández and Senate President Kenneth McClintock, was vetoed by Popular Democratic Party Governor Aníbal Acevedo Vilá, and triggered the constitutional mechanism of keeping the previous year's budget in place.

In 2006, the Governor, in a struggle against the Legislature, ordered a partial shutdown of the government for two weeks, which also imposed new challenges on the office, which saw a succession of three directors during one four-year term.