In August of 1980, H.G. Mor Dionysius Thomas (then metropolitan of Ankamaly diocese and now H.B. Catholicos Mor Baselios Thomas I) visited a handful of Malankara Syriac Orthodox Christian families in Los Angeles and left behind vestments and a censer for celebrating the Divine Liturgy and urged these families to organize a church.

In 1982, His Holiness Patriarch Mor Ignatius Zakka I blessed Malankara with his first apostolic visit after consecration as Patriarch. He was accompanied, among others, by H.E. Mor Athanasius Yeshue Samuel, Archbishop of North America. Rev. Fr. George Parathuvayalil, who was a young and prominent priest of Ankamaly diocese, caught the attention of the metropolitan due to his fluency in Syriac. On returning to the U.S., H.E. Mor Athanasius arranged for Fr. George’s emigration and appointed him to assist at the St. Ephrem’s Syrian Orthodox Church in Los Angeles. With his arrival and with the generosity of the Suryoyo community who offered their church to hold services, a Malayalee Syriac Orthodox congregation was formed with hardly a handful of families. The church was named St. Mary's and the first divine liturgy was held on December 12, 1982, at the St. Ephrem’s Church. On September 6, 1986, H.H. Patriarch Mor Ignatius Zakka I celebrated Holy Qurbono for this fledging parish at St. Ephraim’s Syriac Orthodox Church. For the next seven years, the congregation gathered each Sunday at the St. Ephraim’s Church.

In 1989, St. Ephraim's Church moved to Burbank and St. Mary's Church found a temporary home in the St. John Eudes Catholic Church, Chatsworth, on August 13, 1989. Almost at the same time, Rev. Fr. Mani Rajan replaced Fr. George and served the congregation for the next four years. During these years, the congregation earnestly wished for an independent place for worship. By Easter Sunday, 1992, the parishioners were able to accumulate $100,000 towards buying a church building. A series of what can only be described as Divine interventions then followed which culminated in the acquisition of the current building at 10034 Laurel Ave., Whittier, CA. 

In early 1993, Rev. Fr. Mani Rajan decided to return to India and the church was in danger of being without a priest. A search was initiated and the Rev. Fr. Sabu Thomas was identified. H.E. Mor Athanasius Samuel provided the necessary paperwork and Rev. Fr. Sabu Thomas became the Vicar of St. Mary’s Church.

With a new home and a newly appointed priest the church began a fresh chapter of its history. The first Holy Qurbono at the new location was offered on November 14, 1993. The church was remodeled according to the traditions of the Syriac Orthodox Church in April 1994, just in time for its next momentous landmark in history. On May 14, 1994, His Holiness Moran Mar Ignatius Zakka I Iwas, the Patriarch of Antioch and all the East, consecrated the altars of the church, dedicating the main altar to the Mother of God, and the side altars to Patriarch St. Elias III and St. Gregorios of Parumala.

At the same time, the church became part of the then newly formed Malankara Archdiocese of North America. The church also enjoyed the position of Simhasana Church under the direct administration of the Patriarchate and the spiritual guidance of H.E. Mor Clemis Kaplan from 2002 until 2004 when H.E. Mor Theethos Yeldho was appointed to shepherd the Malankara Archdiocese. In March 2006, the church hosted the clergy conference of the archdiocese presided by H.B. Catholicos Mor Baselios Thomas I.

The congregation has actively contributed to innumerable charitable activities in the USA and India. Through many trials and tribulations, St. Mary's Church has stood steadfast in the faith and traditions of the Syriac Orthodox Church and in obedience to its Supreme Spiritual Head, the Patriarch of Antioch.

The Lord Almighty has showered His blessings abundantly on this humble congregation through the years and the parish continues to prosper through the intercession of the Holy Virgin Mary, Mother of God and its patron saints, Patriarch St. Elias III and St. Gregorios of Parumala.