He is a member of the Liberal Party, the banner of the political opposition. He ran for congressman in 1998 and served as Representative of the 2nd District of Tarlac until 2007. During his term, he served on numerous committees, namely:
- Civil, Political & Human Rights (Vice-Chairman), Public Order & Security, Transportation & Communications, Agriculture, Banks & Financial Intermediaries, Peoples’ Participation, Suffrage and Electoral Reforms, Appropriations, Natural Resources, Trade & Industry (11th Congress)
- Civil, Political & Human Rights, Good Government, Public Order & Security, Inter-Parliamentary Relations & Diplomacy (12th Congress)
- Banks & Financial Intermediaries, Energy, Export Promotion, Public Order & Safety (13th Congress)
He was then elected as Senator in the 2007 midterm elections under the Genuine Opposition, a coalition comprising a number of parties, including his own Liberal Party. With more than 14.3 million votes, Aquino's tally was the sixth highest of the 37 candidates for the 12 vacant seats elected from the nation at large. He assumed his new office on June 30, 2007.