The Governing body of Little Flower Seminary consists of Very Rev. Fr. Superior General, General Councillors, Very Rev. Fr. Provicial Superiors of the four Provinces, Very Rev. Fr. Rector, Rev. Fr. President, Rev. Fr. Dean of Studies and Fr. Econome.
| Superior General | |
| Very Rev. Fr. Jojo Varakukalayil CST | |
| General Councillors | |
| Vicar General | Rev. Fr. George Arancehry CST |
| General Councillor | Rev. Fr. Kapiarumalayil CST |
| General Councillor | Rev. Fr. Anish Angadiath CST |
| General Councillor | Rev. Fr. Jeevan Thundiyil CST |
| Provincials | |
| L.F. Provincial Superior | Rev. Fr. Sabu Kandamkettiyil CST |
| S.T. Provincial Superior | Rev. Fr. Johnson Varakkaparambil CST |
| S.J. Provincial Superior | Rev. Fr. Jijo Indiparambil CST |
| K.J. Provincial Superior | Rev. Fr. George Alukka CST |
| Seminary Administration | |
| Rector | Rev. Fr. Francis Chittinapilly CST |
| President | Rev. Fr. Joby Edamuriyil CST |
| Dean & Registrar | Rev. Fr. Joy Vayalil CST |
| Econome | Rev. Fr. Anto Karakattu CST |