Thattil was appointed and installed as the auxiliary bishop of Thrissur in 2010 to serve along with metropolitan archbishop Andrews Thazhath.

In January 2024, he was elected major archbishop by the Holy Synod of the Syro-Malabar Church to succeed George Alencherry (2011-2023).

On 21 December 1980, Mar Joseph Kundukulam ordained him as a priest for the Archdiocese of Thrissur at his home parish of the Basilica of Our Lady of Dolours.

[5][6] On 23 December 2013, At the Request of Leonardo Sandri and George Alencherry, Pope Francis appointed Thattil as the Apostolic Visitator for all the lay faithful of the Syro Malabar Church living in India outside their own Territory (without an Eparchy of their own).

During his time as Apostolic Visitator, he brought 88 Priests to work in the Mission and served 23 states, 2 Union Territories, and 2 Islands.

[9][10][11] On 9 January 2024, the Synod of Bishops convened and elected Raphael Thattil as the fourth Major Archbishop of the Syro-Malabar Church replacing George Alencherry.