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. Joby Edamuriyil CST |
| S.J. Provincial Superior | Rev. Fr. Francis Chittinappilly CST |
| K.J. Provincial Superior | Rev. Fr. Saju Kuthodiputhenpurayil CST |
| Seminary Administration | |
| Rector | Rev. Fr. Saji Nellikkunnel CST |
| President | Rev. Fr. Tomy Alumkalkarot CST |
| Dean & Registrar | Rev. Fr. Tigi Thanniyil CST |
| Econome | Rev. Fr. Joby Mamalassery CST |