COU-TEDDO began in 2002 following the creation of Kumi Diocese, which was curved out of Soroti Diocese in 2001. Originally it was referred to as Church of Uganda Soroti Diocese Development Office (COU-SDDO) and acted as the development arm of Soroti Diocese. Following her formalization in 2004 overseen by two Bishops Rt. Rev. Dr. Charles B. Obaikol of Soroti Diocese and Rt. Rev. Thomas Edison Irigei of Kumi Diocese, COU-TEDDO was born as a joint development office for Teso sub-region.

Since inception, COU-TEDDO has played critical roles in the development of Teso sub-region over the years by meeting the needs of the community in a holistic manner during the periods when the sub-region went through civil strife, cattle rustling and civil war that disrupted the livelihoods of the communities. Between 1986 and 1992, Soroti Diocese implemented a rehabilitation programme aimed at restoring the livelihoods of the affected communities with support from Church of Uganda Planning, Development and Rehabilitation Office (COU-PDRO) focusing on Agriculture, Health and Education programmes. These programmes were implemented with support from donors such as Christian Aid United Kingdom and Inter-Church Organization for Development Cooperation (ICCO) Netherlands. In 1996, the Church of Uganda Soroti Development Department was then transformed to a semi-autonomous office called COU-SDDO.