In 1993, Fr. Niall O'Brien started meeting the original members of Pax Christi Pilipinas based in Manila.

He also started the formation of a small group of Pax Christi in Negros and among his friends in the other parts of the country.

That was his way of refounding Pax Christi Pilipinas again.

In 1995, Fr. Niall, Simon Gregorio and Cesar Villanueva attended the 50th Anniversary of Pax Christi International in Assisi, Italy. In that International Meeting, Pax Christi International accepted Pax Christi Pilipinas as an aspiring member in becoming a full section of the international movement.

In 1999, during the Pax Christi International meeting in London, Pax Christi Pilipinas was accepted as a full section of the movement and an addition to the membership from the Asia Pacific region joining the Australia and New Zealand sections.

In its Manila meeting in 2000, Deng Guiguinto from Catholic Relief Services Mindanao was elected national coordinator. Deng, however was volunteered to East Timor for some time after her acceptance of the coordinatorship. Apple Santiago Oreta took over as national coordinator until the middle of 2004 and retired Bishop Julio Labayen was elected Bishop President for a term of three years ending in 2004.

In June 2004, Cesar H. Villanueva accepted the work as national coordinator for Pax Christi Pilipinas. Bishop Antonio Ledesma was also invited to be the next President beginning 2005 for a three-year term. Fr. Roberto Layson, OMI was also invited to be the National Chaplain of the movement.

In November 2004, the second General Assembly of Pax Christi Pilipinas was held at the Miriam College hosted by Dr. Loreta Castro of the Miriam Peace Center.

During the assembly, the new vision of the movement was approved and a five member Executive Board was formed.

Pax Christi Pilipinas is a founding board member of the Philippine Action Network Against the Proliferation of Small Arms or PHILANSA.

It has been a strong advocate against the reimposition of the death penalty.

Recently it became a member of Sulong CARHRIHL “Comprehensive Agreement on Respect for Human Rights and International Humanitarian Law”, a new civil society network that seeks to promote the peace process and the observance of an agreement that was signed between the National Democratic Front and the Government of the Republic of the Philippines.