The history of Evangelization in the present Diocese of Muzaffarpur goes back to the 18th century when the Congregation of the Propagation of Faith erected the prefecture of Tibet-Hindustan in 1703 and entrusted it to the Capuchin Fathers of the Italian Province of Picenum in the Marches of Ancona. Father John Francis of Camerion, O.F.M. Cap.was appointed its Prefect.

On March 28, 1980, when Pope John Paul II accepted the resignation of the Bishop of Patna, the same year Patna Diocese was divided into two units, Patna and Muzaffarpur. Father Benedict J. Osta, S.J. succeeded Bishop Augustine Wildermuth, S.J. as the new Bishop of Patna, and Father John B. Thakur S.J. became the first Bishop of the new Diocese of Muzaffarpur.

On June 24, 1980 in Bettiah, Fr. John B. Thakur was consecrated the Bishop of Muzaffarpur. The period from 1980 till 1998 witnessed a marked expansion of the number of people working in the area.A minor seminary was begun in Muzaffarpur.Likewise a number of Sisters, Brothers and Priests congregations opted to come to Muzaffarpur to work in the Diocese. These were serving in 20 parishes with resident priests, 30 Mission Stations, visited by the neighbouring parishes.  High schools, Middle schools, Teacher Training schools and non-formal schools began to abound, as well as Health care Centres and Dispensaries. 

By a decree of His Holiness, Pope John Paul II, dated August 4, 1998, the Diocese of Muzaffarpur was bifurcated, and the new Diocese of Bettiah was created comprising the five districts of East and West Champaran, Gopalganj, Siwan and Saran.

Muzaffarpur Diocese now comprises the following 12 Civil Districts of the State of Bihar: Muzaffarpur, Vaishali, Samastipur, Sitamarhi, Darbhanga, Madhubani, Saharsa, Begusarai, Madhepura, Khagaria, Shivhar and Supaul.