Among Yalung's pastoral assignments were being assistant parish priest in Balibago, Angeles City (1979–1980) and formator at Mother of Good Counsel Seminary in San Fernando, Pampanga (1987–1989). He served as Vice-Rector of the Lorenzo Mission Institute (1989-1991) and as Rector of San Carlos Seminary (1991–1994). He was made Papal Chaplain for the Archdiocese of Manila in 1991.[citation needed]
Pope John Paul II named him auxiliary bishop of Manila on March 23, 1994.[2] Fondly known as Bishop Tom, he headed the Ecclesiastical District of Makati. Concurrently, he served as Parish Priest and Rector of the National Shrine and Parish of the Sacred Heart in San Antonio Village, Makati from 1999 to 2001.[citation needed]
On October 18, 2001, he was named successor to the Most Rev. Protacio Gungon as Bishop of Antipolo.[citation needed] He was installed on December 3 that same year.[4] His tenure as bishop was marked by the major renovation of the Cathedral of Antipolo, under the rectorship of Rev. Fr. Enrico Salazar, the inauguration of Our Lady of Peace and Good Voyage Seminary, and the preparation of the diocese for the upcoming establishment of the neighboring Diocese of Pasig. Around more than 10 parishes (and quasi-parishes) were established during his episcopacy.[citation needed]
Yalung's term was interrupted when a scandal broke out. He was discovered to have fathered a child.[5] The incident prompted him to resign on October 19, 2002.[3] His resignation was accepted on December 5, 2002.[4]
Post-resignation
After his resignation, the Vatican named the Most Rev. Jesse E. Mercado, D.D., former Auxiliary Bishop of Manila (now Bishop of Parañaque), to become the diocese's erstwhile apostolic administrator pending the appointment of a new bishop, which came on December 7, 2002, with Kalibo Bishop Gabriel V. Reyes' designation as the third Bishop of Antipolo.
Yalung would work as a Social Worker in the United States, where he fled following the scandal. He had a second daughter with his lover,[6] who announced that Yalung would leave the clergy to attend to their children.[7]