The Mar Thoma Christians migrated from Kerala to Udaipur, after which they felt a necessity of having a place to worship. Thus, they formed “Malayalee Syrian Christian Congregation” which accommodated Mar Thoma and Orthodox Christians. Rev. K. V. Varkey, of Mar Thoma Church Valsad, Gujarat was the first Mar Thoma vicar who visited Udaipur and conducted Holy Communion on 4th September 1966 at the Shepherd Memorial CNI church, Udaipur.
The desire of the Martomites was fulfilled on 6th March 1993, and Rev. Geeverghese Mar Athanasius, Bombay-Delhi Diocesan Bishop laid the foundation stone of Emmanuel Mar Thoma Church Udaipur & the dedication ceremony by Rt. Rev. Dr. Issac Mar Philoxenos Episcopa on 27th August 1994.
Later, the members felt the need to have a separate room for the guests who visited the parish. The construction of the guest room was completed in the year 1998.