Since the two Portuguese Jesuit Missionaries, Cabral and Cacella had travelled through Brahmaputra on their way to Tibet in 1626, many missionaries had passed through the present territory of the Diocese of Bongaigaon. However, the first to take up residence in the present diocese area were the Salesian Fathers Archimede Piannazzi and L. Rocca, who were appointed to work among Garos. In 1932 they took up residence at Dhubri and used it as a base for their apostolate in the Garo Hills as Catholics were denied permission to work in that area. On September 8th, 1933 Mgr. Louis Mathias decided to open a centre in Tura in Garo Hills and Fr. Piannazzi and Fr. Rocca were told to go there from Dhubri and a decision was taken to shift the centre from Dhubri to Barpeta Road which was more central. Mgr. Louis Mathias with Fr. Rocca visited Barpeta Road on February 20, 1933 and entrusted Mr. Andrews, the responsibility to purchase a plot of land for the purpose of establishing a mission centre. On May 23, 1933 a plot of land was acquired for the mission and on June 3, 1933, Mgr. Mathias declared the new mission opened and Fr. Scuderi was given the charge to look after the mission from Guwahati. 

A priest began to reside at Barpeta Road in 1936. At that time its territory covered the whole area of the present diocese and more. The present progress can be attributed to Bishops Orestes Marengo, Joseph Mittathany, and Robert Kerketta and to Fr. Remo Morra SDB. Under the leadership of Archbishop Thomas Menamparampil, the area had further growth which led to the creation of the  Diocese of Bongaigaon. Fr. Joseph Zubizzaretta SDB’s name will be always remembered among the most outstanding missionaries of the area.

The Diocese of Bongaigaon is created on the 10th of May 2000, and was carved out of the Archdiocese of Guwahati consisting of Nalbari, Barpeta, Bongaigaon,South Salmara- Mankacher, Dhubri, Kokrajhar, Chirang districts and two subdivisions of Baksa district namely Salbari and Mushalpur of lower Assam. It covers the surface area of 13,630 sq. km. with an overall population of 5.5 million of which 69,620 (1.2%) are Catholics. There are 34 parishes, 37 Diocesan priests,48 Religious Priests, 10 Brothers and 223 Women religious. Catholic population is mainly tribals.  Bodos, Santhals, Adivasis, Garos, and Rabhas are the major groups. General population comprises of Koch and Koch Rajbanshies, the Assamese and the Bengalis. Dhubri and Barpeta districts have 56% and 39% Muslim population respectively, according to 2011 Census.

The Diocese of Bongaigaon runs 52 educational institutions at primary level, 6 at secondary level, 1 at tertiary level. In the field of health care the diocese runs 16 dispensaries at primary level and 1 hospital at secondary level. Besides the diocese runs 60 boarding houses for boys and girls and has a social service department – BGSS – which takes care of the developmental works in the diocese. 

Within the territory of the diocese there are some important historical places. The Koch dynasty had its origin at Chikna Mountains. The beginning of the Koch dynasty can be traced to Hariya Mandal a Mech chief, who married two sisters Hira and Jira, the daughters of Hajo, a Koch chief. Hariya Mandal’s domain was in Chikna mountains situated between the Sankosh River and the Champabati River, about 80 kilometers north of Dhubri in the erstwhile undivided Goalpara district of Assam. Bisu, who was to later become Viswa Singha, was born to Hariya Mandal and Hira.

Kajigaon, the birthplace of Kalicharan Brahma is also in the parish of Basbari. Kalicharan Brahma (1862-1938), originally Kalicharan Mech, was a 20th-century social and religious reformer of Bodo society.  

One of the eight civil districts which constitute the territory of the diocese, Barpeta is renowned in the historical map of Assam as the “Land of the Satras”. These Satras bear the testimony of the great Assamese reformer, saint, scholar and cultural exponent Srimanta Sankardeva and his able disciple Shri Shri Madhabdeva who arrived from Upper Assam back in the 16th century to lay down strong foundation of Assamese Culture in the region through his socio-religious Vaishnava-reform movement. With the advent of Shrimanta Sankardeva Barpeta region turned into a place of great religious importance. Large number of Satras was established by the disciples of this great Vaishnava saint. This reform movement left a historic legacy. The Barpeta Satra and various other Satras scattered around the district attract devotees from every nook and corner of Assam, particularly during festivals and anniversaries. Among the Satras that are regularly visited by outsiders are Barpeta, Patbaushi, Sundaridiya, Sunpura, Ganak Kuchi, Satra Kanara and Jania. 

On the north the diocese is bounded by the kingdom of Bhutan. There are 18 passages or gateways through which the Bhutanese people can communicate with the people living in the plains. These Dooars belonged to the Koch Kingdom; and taking advantage of the weakness of the Koch kingdom in subsequent times, Bhutan took possession of the Dooars. This region was controlled by the kingdom of Bhutan when the British annexed it in 1865 after the Bhutan War under the command of Captain Hedayat Ali. This region is divided by the Sankosh river into the Eastern and the Western Dooars, consisting of an area of 8,800 km (3,400 sq mi). The Western Dooars is known as the Bengal Dooars and the Eastern Dooars as  The eastern part was merged with Goalpara district in Assam and the western part was turned into a new district named Western Dooars. Again in the year 1869, the name was changed to Jalpaiguri District. After the end of the British rule in India in 1947, the Dooars acceded into the dominion of India and it merged with the Union of India shortly afterwards in 1949.

Three of the nine rivers that are national  waterways in Assam flow through teritory of the Diocese. They are Gangadhar, Ai and Beky.

On the south, the diocese is bounded the Rangpur division of Bangladesh.

On the 20th of August 2000, Bishop Thomas Pulloppillil was ordained as the first Bishop of the newly erected diocese of Bongaigaon.