Members of this church are direct descendants of the Thomas Christians that the Portuguese encountered in 1498 while exploring the Malabar coast of India (now the state of Kerala). As mentioned in the History of Christianity in Kerala, they were in full communion with the Assyrian Church in Persia. But they greeted the Portuguese as fellow Christians and as representatives of the Church of Rome, whose special status they had continued to acknowledge despite centuries of isolation.

With the arrival of the Portuguese explorer, Vasco De Gama to Calicut on the Kerala Coast in 1498,  a Latin connection began to take shape among the St.Thomas Christians. The Portuguese were happy to discover the St.Thomas Christians on the West coast of India,  but did not like their connection to East-Syrian Church.    Pointing out some expressions in their liturgical texts, the Portuguese alleged that St.Thomas Christians believed in the Nestorian Heresy. The Synod of Diamper (Udayamperoor) in 1599 convened by the Latin Archbishop Menezes of Goa brought an end to the connection between St.Thomas Christians and East-Syrian Church. St.Thomas Christian Church, thus became a colonial Church of the Portuguese.

In general, however, the Portuguese did not accept the legitimacy of local Malabar traditions, and they began to impose Latin usages upon the Thomas Christians. At a synod held at Diamper in 1599 under the presidency of the Portuguese Archbishop of Goa, a number of such latinizations were adopted, including the appointment of Portuguese bishops, changes in the Eucharistic liturgy, the use of Roman vestments, the requirement of clerical celibacy, and the setting up of the Inquisition. This provoked widespread discontent, which finally culminated in a decision by most Thomas Christians in 1653 to break with Rome. In response, Pope Alexander VII sent Carmelite friars to Malabar to deal with the situation. By 1662 the majority of the dissidents had returned to communion with the Catholic Church.

The Latin connection also brought division to the St.Thomas Christians. The Coonan Cross Oath in 1653 at the Church of Our Lady of Life at Mattanchery was the culmination of several years of latinization by the Portuguese, and the crowd gathered there took an oath that they would not be subject to the Portuguese appointed Archbishop of Goa, Francis Garcia owing allegiance to the pope of Rome. This revolt eventually split the Church into two. A major body of Thomas Christians however went back to Roman supremacy after soothing counter measures taken by Carmelite missionaries. However an equally significant group appealed and eventually established contact with the Antiochene Syrian Non-Chalcedonian Patriarch. The former later got organized into what is the Syro-Malabar Church of today.

After the Coonan Cross Oath, Rome began to take an active interest in the Kerala Christians. Several Carmelite monks were sent to Kerala and Carmelite Vicar Apostolics were residing at Varapuzha. Also, the Portuguese nominated administrators or archbishops for Malabar who were stationed at Kodungalloor. This dual jurisdiction also was cause for complaints to Rome. In 1787, Representatives from 84 churches assembled in Angamaly and drew up a document called Angamaly Padiyola which made a strong demand to Rome for native bishops, citing the sins of omission and commission of the foreign missionaries. In 1861, the arrival of a Chaldean Catholic bishop, Thomas Rokkos sent by the Chaldean patriarch created more problems. He was excommunicated on his arrival by the Vicar apostolic of Varapuzha, and a schism followed. Another Chaldean bishop, Elias Melus arrived in 1874 and he too met the same fate. The Syrian Christians, popularly known as the Surais, in and around Thrissur who owe allegiance to the Syrian Nestorian patriarch are the followers of the schism Melus created.

Finally in 1887, Pope Leo XIII decreed the separation of Rite of St.Thomas Catholics from that of the Latins. Two Vicariates apostolic, at Thrissur and Kottayam with two Latin Bishops, Adolf Medlycott and Charles Levigne were erected. Continued pleas for native bishops reslulted in Pope's decree in 1896 for the erection of three vicariates for St.Thomas Catholics: Thrissur, Ernakulam and Changanassery under Indian Bishops John Menachery, Louis Pazheparambil and Mathew Makil respectively. In 1911, Pope Pius X erected a fourth vicariate at Kottayam for the Southists or Knanites, who claim to be descendents of East-Syrian Christians who migrated from Persia along with Kannai Thomman.

In 1934 Pope Pius XI initiated a process of liturgical reform that sought to restore the oriental nature of the heavily Latinized Syro-Malabar rite. A restored Eucharistic liturgy, drawing on the original East Syrian sources, was approved by Pius XII in 1957 and introduced in 1962. Despite a reaffirmation of the main lines of the 1962 rite by the Oriental Congregation in 1985, however, there has been strong resistance to this reform. The majority of Syro-Malabar dioceses still use a rite that in externals is hardly distinguishable from the Latin Mass. In January 1996 Pope John Paul II presided over the opening of a special synod of bishops of the Syro-Malabar Church in Rome which was to attempt to overcome factional disputes that have centered on the proposed liturgical reforms. In 1998 Pope John Paul II gave the Syro-Malabar bishops full authority in liturgical matters in a further effort to facilitate a resolution of the dispute.

Until recently there was no single head of the Syro-Malabar Catholic Church, but two metropolitan dioceses (Ernakulam and Changanassery) of equal rank. But on December 16, 1992, Pope John Paul II raised the Syro-Malabar Church to Major Archiepiscopal rank and appointed Cardinal Anthony Padiyara of Ernakulam-Angamaly as the first Major Archbishop. He retired in 1996, and was succeeded by Archbishop Varkey Vithayathil in December 1999.

Today, there are 24 Syro-Malabar dioceses in India, 12  of them in Kerala and 12 of them outside the state. There are six organized Syro-Malabar Catholic communities in the United States and one in Canada.

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