The central archives as they are organized today are a result of the passage of Republic Act 9470 in 2007, but its roots can be traced back to at least the 19th century during Spanish rule.

Before that time, the vast majority of the colonial records were scattered among the islands and held in mostly religious centers of the Catholic Church.

[4] The Archive's responsibilities included to plan, develop, and coordinate government-wide programs, policies, rules, and regulations governing the use, storage, and disposition of current operating records of permanent or historical value.

[5] The bureau was represented by its director, historian Domingo Abella, in the International Council of Archives and its Southeast Asian Branch (SARBICA).

On May 21, 2007, more than a century since its establishment, President Gloria Macapagal-Arroyo signed Republic Act 9470 that defined the various functions of the agency and formally renamed it to become the country's National Archives.

Manapat was cleared of the charges by the Sandiganbayan (a special court in the Philippines) in 2005, but he had been on leave shortly before the Senate investigation started a year earlier.

The Archives is currently headquartered in the National Library of the Philippines and maintains offices and facilities in Paco, Manila, Cebu, and Davao.

[10] Some of the oldest records in the archive date back to the rule of the first Spanish Governor-General to the Philippines, Miguel López de Legazpi (1564–1572).