It was founded on October 11, 1898, shortly after news that the Treaty of Paris would be signed, ending the Spanish–American War and transferring the Philippines from Spanish to American sovereignty.

Shortly after the paper's founding, reports reached Manila about the Paris Conference that would lead to the treaty where Spain ceded its claim over the Philippines to the United States.

[3] On February 5, 1986, The Manila Times re-opened, several days before the People Power Revolution that ousted Marcos and installed Corazon Aquino as president.

[3][6] In 1999, The Manila Times faced controversy when it published a story about President Joseph Estrada, who was described as an "unwitting godfather" in a deal between the National Power Corporation (NAPOCOR) and Argentine firm Industrias Metalurgicas Pescarmona Sociedad Anonima (IMPSA) [es].

[7][3] On March 9, Estrada filled a libel suit against The Manila Times; the owners printed an apology on its front page, triggering the resignation of the paper's editors and writers.

[11][3][12] On May 14, 2001, Mark Jimenez acquired the paper, until he sold to Dante Ang, a publicist for President Gloria Macapagal Arroyo on August 8, 2001.

Puno defeated 2nd choices OFW, Governor Eddie Panlilio, the Filipino Nurse, the DSWD social worker, the Pinoy Farmer, Manny Pacquiao and Joey de Venecia.