The church in Kerala traces its origin to the preaching of St. Thomas, one of the twelve Apostles of Jesus Christ. In 4^th century, the Church in Kerala came in contact with the Syro-Chaldean Churches and consequently adopted the Syrian Liturgical tradition in its worship, and in 16^th century it was influenced by Western Church through its missionaries. Owing to the policy of the Portugese missionaries in Latinizing the Liturgy and indigenous customs of the Apostolic Indian Church, a section of the community broke away from the Portugese ecclesiastical authorities and eventually united with the Jacobite Patriarch of Antioch.

In 1926 the Episcopal Synod held at Parumala, empowered Metropolitan Mar Ivanios to enter into negotiations with Rome to effect a re-union with the Catholic Church under expressed condition that the ancient and venerable traditions of the Malankara Church should be retained and kept intact. The Holy Father Pope Pius XI graciously accepted the conditions and welcomed the re-union. Accordingly on 20 September 1930, Archbishop Mar Ivanios, Bishop Mar Theophilos, Rev. Fr. John Kuzhimepurath O.I.C., Deacon Alexander (later Fr. Seraphion O.I.C.) and Mr. Chacko Kiliyelathu made their Profession of Faith and were duly received in the Catholic Communion by His Excellency Rt. Rev. Dr. Maria Benziger, Bishop of Quilon, specially deputed by the Holy See.

In 1932, His Grace Mar Ivanios visited Rome and His Holiness Pope Pius XI invested him with the Sacred Pallium. By the Apostolic Constitution, "Christo Pastorum Principi" (11 June 1932) the Holy Father established the Syro-Malankara Catholic Hierarchy comprising the Metropolitan Eparchy of Trivandrum and the Eparchy of Thiruvalla. The Metropolitan Eparchy of Trivandrum was inaugurated on 11 May 1933 and His Grace Mar Ivanios enthroned as its first Archbishop. The Eparchy of Thiruvalla was inaugurated on 6 November 1933 and Most Rev. Jacob Mar Theophilos took charge as its first Bishop. On 29 November 1937, Most Rev. Joseph Mar Severios of the Orthodox Church and Most Rev. Thomas Mar Daiscoros, Metropolitan of the Knanaya Jacobite Church, reunited with Malankara Catholic Church.

The pioneer of the re-union movement in Kerala, His Grace Archbishop Mar Ivanios called for his eternal rest on 15 July 1953. Before his death, Rt. Rev. Benedict Mar Gregorios was consecrated as the Auxiliary Bishop, and later the Archbishop. After the successful 41-years of devoted service, he was called for his eternal reward on 10 October 1994. Most Rev. Cyril Mar Baselios, the Bishop of Bathery was enthroned as Metropolitan Archbishop of Trivandrum and as the head of the Malankara Church on 14 December 1995.

His Excellency Most Rev. Joseph Mar Severios was appointed as the Bishop of the Diocese of Thiruvalla in 1951. He was called for his eternal rest on 18 January 1955. Later the eparchy was blessed with the glorious services of Most Rev. Zacharias Mar Athanasios, Rt. Rev. Isaac Mar Yoohanon and Rt. Rev. Geevarghese Mar Timotheos.

The Eparchy of Bathery was inaugurated on 28 October 1978 and His Excellency Most Rev. Cyril Mar Baselios took charge of the diocese officially. His Excellency Most Rev. Paulos Mar Phileoxinos, the Metropolitan of Malabar Independent Church, united into the Syro-Malankara Catholic Church on 28 August 1977. The Eparchy of Marthandam was inaugurated on 16 December 1996 and Most. Rev. Lawrence Mar Ephrem was appointed as its first Bishop, and he was succeeded by Most. Rev. Yoohanon Mar Chrysostom. Bifurcating the Eparchy of Thiruvalla, the Eparchy of Muvattupuzha was inaugurated on 15 January 2003 and Most Rev. Thomas Mar Koorilos was appointed as its first Bishop. On 29 March 2003, Bishop Mar Timotheos resigned due to super-annuation and Mar Cleemis was appointed as the Bishop of Thiruvalla. On 5 January 2005, Most Rev. Joseph Mar Thomas was appointed as the Auxiliary Bishop of Trivandrum and Apostolic Visitor to North America and Europe.

The day, 10 February 2005 is engraved in golden letters in our history – the Syro-Malankara Catholic Church was raised to the status of a Major Archiepiscopal Church. The Hierarchical Head of the Church is elevated as Major Archbishop who exercises patriarchal powers and governs the church assisted by the Holy Synod of Bishops of the Church. The Major Archbishop also assumes the title "Catholicos" according to the Antiochene Malankara tradition. On 14 May 2005, the Major Archbishop Moron Mar Cyril Baselios was enthroned as the first Catholicos.

The Eparchy of Thiruvalla was raised as Metropolitan Eparchy on 14 May 2006, and Most Rev. Issac Mar Cleemis was appointed as the Metropolitan Archbishop of Thiruvalla.

In the course of the growth and development of the Syro-Malankara Catholic Church, besides the canonical institutions, various associations such as the MCYM, MCA, the Legion of Mary, Matruvedi, Pithruvedi and other pious associations have become the backbone of the life of the church.