The diocese was created by Pope John Paul II on December 7, 2002, by virtue of his Apostolic Constitution Animarum Utilitati,[2] and was canonically erected on January 16, 2003, from the Archdiocese of Manila.

Soon after the establishment of the new town, Manila Archbishop José Julián de Aranguren decreed the creation of its parish on September 24, 1856.

The growth of the Catholic faith in the area would be evidenced by the establishment of parishes in Fairview (1975), Lagro (1977), and Bagbag (1978) – which took place during the early years of leadership of Cardinal Jaime L. Sin, Archbishop of Manila.

Pope John Paul II established the Diocese of Novaliches on December 7, 2002, by virtue of the apostolic constitution Animarum Utilitati and appointed Bacani as its first residential bishop.

This news was announced by Cardinal Sin during a conference of the clergy and lay leaders held at Villa San Miguel in Mandaluyong.

The decree also declared that the episcopal seat of the new diocese would be the archdiocesan shrine and Parish of the Good Shepherd along Regalado Avenue, Fairview, Quezon City.

In solemn rites held at the Good Shepherd Parish-Shrine on January 16, 2003, the new Diocese of Novaliches was canonically erected, with Bacani being installed as its first bishop, coinciding his 63rd birthday.

He named Gerardo Giovanni Tapiador as the diocese's first vicar-general, Jaime Lara as chancellor, and James Gaa as Oeconomus or treasurer.

Bacani led the beginnings of the pastoral commissions or ministries in the diocese through the involvement of active lay members of the Council of the Laity of Novaliches (CLaN), which he created on March 21, 2003.