Arthunkal was the capital of Muthedath Kingdom, one of the pricipalities of Kerala, during the 16th century. Historians opine differently as to how Arthunkal got that name.

One among them is that it has evolved from 'Arthikulangara', the name of the place at that time. Arthikulangara, in course of time turned 'Arthikulangal' and later on, Arthunkal.

According to historian George Schurhammer, the capital of Muthedath was known as 'Muthedathunkal' (at Muthedath) and it changed to 'Edathunkal' and then Arthunkal. Portuguese Missionaries landed in Kerala following the arrival of Vasco da Gamma. They visited Muthedath and found so many St Thomas Christians here. They were not baptized, but their ancestors were. The Jesuit missionaries started their mission in Muthedath and Elayedath(the neighbouring principality). In 1579 A.D., the Jesuit priest Manuel Texeira from Goa visited Arthunkal on his way from Kochi to Kollam (Quilon). As on request by the Christians, he arranged Fr Gasper Pius to be appointed in Arthunkal for their spritual services in 1581.

Since 1560 A.D., the Christians and missionaries had been requesting the Muthedath King for the permission of an oratory, though the king did not give much attention to. But following the incessant pestering from the Christians and considering the helps the king had from the missionaries, he granted permission in November, 1581 to construct a church using wood and coconut leaves. He also granted a few trees from his premises for the purpose.

The Christians installed a wooden cross and constructed, with the co-operation of the local Hindus, a church, where the king had given permission to. On 30th November, the church was consecrated in the name of St Andrew the Apostle. The first vicar was Fr Gasper Pius S.J. On completion, the king of Muthedath came to visit the church and asked the vicar to maintain the church suitably to be the House of God. Since then, many Hindus from the neighboring regions came to the church, prayed to St Andrew and got their appeals fulfilled.

In November, 1582, Fr Gasper Pius died of exessive hardwork, hot climate and malnutrition. Another Jesuit priest took charge of the church, but stayed in Kochi. On 30th November, 1583, on the feast day of St Andrew, 500 St Thomas Christians were baptized. They were later known as 'Anjootikkar' (The Five Hundred People). A nair knigt with his 20 soldiers embraced Christianity on the same day, in presence of the King of Muthedath. In 1584 A.D., Fr Jacomo Fenicio S.J. was appointed vicar of Arthunkal. He started the construction of a new church in stone and lime, with permission of the King, and completed it in 7 years. After Fr Fenicio was transferred to Kozhikode, eight priests took charge in succession. Fr Fenicio was appointed again in 1619, and in the next year, he reconstructed the church. He was much loved and was considered a holy man by the people and the administrators. People called him saint and 'Veluthachan', meaning white father. 'Veluthachan' later became the popular name of St Sebastian. Fr Fenicio said to have performed lots of miracles while he was still alive. Even Hindus believed in the power of his prayers and approached him for his blessings. He was known as the second Apostle of the east and died in 1632. Huge was the crowd including kings flowed in, to pay him the final tribute. His body was buried inside the church and people used to pray and light candles there. The tomb is still preserved near the altar of the old church.

Fr Fonsaco, who took charge after Fr Fenicio, reconstructed the church in 1640 with the elevation facing west. It is during his time, that the Miraculous statue of St Sebastian reached from Milan. In the fall of 18th century, the church was taken charge by Carmelite missionaries. During their service or rather on 29 November, 1829, St. Chavara Kuriakose Elias was ordained by Rt Rev. Dr Staballini, the then bishop of Verapoly who was residing at Arthunkal Church.

In the second half of the 19th century, Fr Gasper Bylon de Mariatoris Kaithavalappil was appointed vicar, to be the first local priest to take charge of Arthunkal Church. During the vicarship of Fr Vincent Das Navis, in 1910, foundation stone for the present new church was laid.

Fr Sebastian Presentation who was considered a holy priest, Msgr Silvarius Jackson who later became the first Vicar General of the diocese of Alappuzha and Msgr Daniel Kurisunkal who completed the construction of the present church, were the successors. Msgr Daniel Kurisunkal was followed by Msgr Peter Karumancherry, Msgr Andrew P. Thekkeveedu, Rev. Dr Dominic Koilparambil, Rev. Fr Paul Arackal and Rev Fr Marian Jose Pereira.

Fr. Stephen J Punnackal is the Rector, Vicar forane and parish priest of Basilica and his assistants are Fr. Cyrus Thomas Kattungalthyil and Fr. Micheal George Arayanparambil. Fr. George Bibalan Arattukulam is the chaplain of St. Rita's Church.