The LCU organizes her individual members into local churches Under Regional Deaneries subordinate to the National Synod Conference, in order to fully implement and advance her Vision, Mission, Objectives, and all the Confessions of the Evangelical Lutheran Church.
Currently there are over 150 congregations distributed in 7 Deanries of LCU including Central, Eastern, Far- East Deanery, Mid-Western, North- Eastern, Northern and South- Western Deanaries s[praed in all the four mayor administrative regions of Uganda.
The LCU works to serve, support, and enhance the spiritual wor, growth, and wellbeing of all members congregations, without which the LCU AND nsc would not exit. As one of the Synodical body we confess together the Word of God and Worship One Ecclesiasticl Unit.
A table showing Regional distribution of Lutheran Churches/ Congregations& Preaching Stations
| NO | LCU Deanery | NO of Churches/ Congregation& Preaching Stations |
| 1. | Eastern Deanery | 56 Congregations & 5 Preaching Stations |
| 2. | Far- Eastern Deanery | 4 |
| 3. | Central Deanery | 9 |
| 4. | Mid- Western Deanary | 19 |
| 5. | South – Western | 21 |
| 6. | Northern Deanery | 5 |
| 7. | North Eastern | 25 |
| TOTAL | 144 |
CHURCH GOVERNANCE AND ADMINISTRATIVE STRUCTURE
The Church is Governed and Administered under the following Organs;
- The National Synod Conference (NSC); This is the supreme governing authority of the Church, it comprises of the House of Clergy, House of Laity, the Women’s and Youth leagues.
- National Synod Board of Trustees; This acts on behalf of the National Synod Conference in all matters whatsever, and is the executive arm of the the Church headed by the National Presiding Bishop.
- Regional Synod Conferences/ Deaneries; Are the Regional subdivisions of the church, under which Churches/ Congregations are grouped on a regional terrotorial basis. these are headed by Deans who serve under the National Synod Board of Trustees.
- Local Congregations/Churches; These are the smallest Administrative grouping and spiritual units of the LCU, under which the Lutheran individual members are organised, congregate and gather. Regional groups of congregations from regional Synod Conferences/ Deanaries. The Local congregations constitute the National Synod Conference.
- Clergy, Laity, Women, Youth and Children; The LCU is also organised under the following organs; Colleges f Clergy, college of Laity, Women’s league, Youth league and the children’s ministery. These are groupings allow the LCU to nationally organise ministry programmes that focus on each Category effectively.
- Counsel of Elders; This is composed of seasoned men and women of the LCU who had served at the National level for over ten years. These men and women offer counsel, arbitration and mitigation at all church levels especially in times of conflict.
