After the proclamation of th Philippine Independence from Spain on June 12, 1898 at Kawit, Cavite, the Second Revolutionary Governemnt under the leadership of President Emilio Aguinaldo was born. On September 26, 1898, Aguinaldo issued a Decree reorganizing the existing departments of the government and appointed Gregorio Araneta as the first Secretary of Justice on the same day. The Department of Justice traces its beginning to this Decree.

Under American rule, the Department was renamed at different times as the "Office of the Attorney of the Supreme Court" (1899), "Office of the attorney General"(1901) and "Department of Finance and Justice" (1901), In 1916, the Department of Justice was reestablished and given administrative supervision over inferior courts. It continued to function as such under the Philippine Commowealth (1935).

When the Japanese forces overran the Philippines in 1942, the Department was transformed into a Commission. Under the civilian government established by the Japanese, it became a Ministry.

In 1947, a year after the Philippines attained independence, the Department of Justice was reestablished. When a parliamentary system of government was set up in 1973, it again became a Ministry. At the same time, it was divested of its supervisory authority over the lower courts.

The Department of Justice was reborn under the Presidential form of government provided in the 1987 Constitution.