Although Catholic presence in Northeast India can be dated back to 16th century, the history of Shillong Archdiocese begins in 1889 when the new ‘Prefecture Apostolic of Assam’ was entrusted to the Society of the Divine Saviour (popularly known as Salvatorians).

The first group of 4 under the leadership of Fr. Otto Hopfenmueller SDS, the Mission Superior, arrived in Shillong in February 1890. Fulfilling the wish of Propaganda Fide, and also being advised of greater possibilities for Church growth in the Hills, they chose Shillong as the seat of the Prefecture. Fr. Christopher Becker SDS became its first Prefect Apostolic in 1906.

Following their repatriation during World War I (1915), the Jesuits of Calcutta looked after the pastoral needs of the Prefecture, until it was entrusted to the Salesians of Don Bosco who under the leadership of Rev. Fr. Louis Mathias SDB took charge of the Prefecture in January 1922. Considering the rapid growth of the Church in Northeast India, the Holy See raised the Assam Prefecture to the status of a diocese on 9th July 1934, appointing the then Prefect Apostolic, Rev. Fr. Louis Mathias as its first bishop.

After Bishop Louis Mathias was transferred as archbishop of Madras on 1st April 1935, Mgr. E. Bars SDB functioned as its Vicar Capitular for a short period of time. Bishop Stephen Ferando, SDB, then bishop of Krishnagar, was transferred to Shillong and took charge as its second Bishop in January 1936. On 23rd July 1951, Shillong was bifurcated to form the Dibrugarh diocese, followed by Tezpur diocese in 1964. In 1969, Bishop Stephen Ferrando retired. Subsequently, Shillong was elevated to the status of an archdiocese, with dioceses of Dibrugarh, Tezpur and Silchar (later renamed as the diocese of Aizawl) as its suffragans. It was first called the Archdiocese of Guwahati-Shillong, but then was renamed as the Archdiocese of Shillong-Guwahati in order to reflect the growing Catholic presence of Shillong. Most. Rev. Hubert D’Rosario SDB was its first Metropolitan Archbishop.

Due to the rapid growth of the Church, the Archdiocese went through further divisions to form the dioceses of Tura (1973), Diphu (1983), and Guwahati (1992). Rev. Fr. Tarcisius Resto Phanrang SDB was appointed Auxiliary Bishop of Shillong- Guwahati in 1990, when the Catholic Church in Northeast India celebrated the centenary of the establishment of the Assam Prefecture.

After Archbishop Hubert D’Rosario passed away on 30th August 1994, Bishop Tarcisius Resto Phanrang became Diocesan Administrator, and later on, was appointed Archbishop of Shillong on 1st August 1995. Following his death on 5th May 1999, Rev. Fr. Michael Marbaniang was elected as the Diocesan Administrator. On 2nd April 2000, Rev. Fr. Dominic Jala SDB was ordained bishop and took charge as Archbishop of Shillong.

The Archdiocese of Shillong was further bifurcated with the establishment of the dioceses of Nongstoin and Jowai (2006). On 2nd April 2006, Apostolic Nuncio Most Rev. Pedro Lopez Quintana ordained Rev. Fr. Victor Lyngdoh and Rev. Fr. Vincent Kympat as the first bishops of the new dioceses. After the tragic death of Archbishop Dominic Jala on 10th October 2019 in USA, Rev. Fr. John Madur served as the Diocesan Administrator until 2021.

On 28th December 2020, Most Rev. Victor Lyngdoh, then Bishop of Jowai, was appointed Archbishop of Shillong and was installed on 6th February 2021 at the Cathedral of Mary Help of Christians, Laitumkhrah.
On 8th February 2025, Rev. Fr. Bernard Laloo was appointed Auxiliary Bishop of Shillong and was consecrated on 30th March 2025 by Archbishop Victor Lyngdoh in the presence of Archbishop Leopoldo Girelli, Apostolic Nuncio to India and Nepal.

At present, the Archdiocese of Shillong comprises East Khasi Hills District and Ri Bhoi District, Meghalaya, having 45 parishes.