St. Francis Xavier arrived in Malacca in 1545. From then until his death in 1552, he visited Malacca five times. In 1548, while in Goa, he sent to Malacca Fr. Francisco Perez and Bro. Roque de Oliveira. They established the first Jesuit Residence and a school.

The Jesuits were expelled from Malacca together with other clergymen and religious after the fall of the city to the Dutch in 1641.

In the mid – 20th century, Jesuit presence in Malaya resumed with the arrival of two French Jesuits, Frs. Andrew Joliet and Monsterleet, who were expelled from Communist China in 1949. Fr. Andrew worked for a while in the Church of the Sacred Heart before moving north to the Church of the Holy Rosary in Kota Bahru, Kelantan. Fr. Monsterleet did catechetical work among school children at the Church of Sts. Peter and Paul, Singapore for a few months.

Following in their footsteps were other Jesuits. In October 1951, Fr. Patrick Joy was appointed superior of the Jesuits in Malaya and arrived in Singapore on 17th November 1951. Due to his vision and industry a Jesuit community was established and Kingsmead Hall Hostel was completed in June 1954. In January 196l, the Church of St. Ignatius was completed and opened.

In 1955, the Diocese of Malacca was divided into three dioceses. The Bishop of the newly erected diocese of Kuala Lumpur, the Rt. Rev. Dominic Vendargon, invited the Jesuits to work in his diocese. Fr. Paddy Joy came up from Singapore and applied to the authorities in Petaling Jaya for land on which to build a Church and a Youth Leadership Centre. He was later joined by Fr. Edward Bourke, who was involved in the complicated negotiations concerning the site of the Church.

Fr. Joy returned to Ireland in 1958. Before he left Malaya, Fr. Paddy McGovern and Fr. Geoffrey Murphy came down from Hong Kong to continue the work begun by Fr. Joy. In May 1961, the Youth Centre, Xavier Hall, was completed. Fr. McGovern, chaplain to the Army in Kuala Lumpur, was a tireless fund-raiser for the new church while Fr. Murphy saw to the many practical details involved in the construction.

The Church of St. Francis Xavier was officially opened on 2nd February 1961 by His Lordship Dominic Vendargon, the Bishop of Kuala Lumpur. Fr. Murphy was installed as the first Parish Priest. He was assisted by Fr. McGovern and Fr. Paul Jenkins. A few months later Fr. Edmund Sullivan and Fr. Joseph Garland joined the Jesuit community in Petaling Jaya. Fr. Sullivan did great work in Sungai Way New Village, saying Mass in a private house every Sunday evening and teaching catechism to children.

In 1963 the Bishop of Kuala Lumpur asked the Jesuit fathers to take over the Church of the Assumption, which had been opened in 1960. Fr. Richard Harris and Fr. Patrick Grogan arrived to take on this responsibility, thus putting all 4500 Catholics in Petaling Jaya at that time under the care of the Society of Jesus.