On July 3, 2015 Pope Francis assigned Monsignor Villarojo as one of the auxiliary bishops of Cebu. He was consecrated bishop on 10 August 2015 at the Metropolitan Cathedral of the Archdiocese of Cebu. He was ordained by Archbishop José S. Palma, the current Ordinary of the Archdiocese.
On May 14, 2019, Pope Francis has assigned Bishop Villarojo as the new bishop of the Diocese of Malolos. He was put in position on August 21, 2019 by Luis Antonio Tagle, Archbishop of Manila together with Gabriele Giordano Caccia, then Apostolic Nuncio to the Philippines.