 | Patrick Foy Esq. | 1st Principal - College founded firstly as Jaffna Catholic English School | 1850 - 1858 | |
 | Rev. Bro. John Joseph Brown OMI | Renamed Jaffna Boys Seminary | 1859 - 1861 | Date of Death - 29 March 1885 |
 | Rev. Bro. Patrick Joseph Conway OMI | | 1862 - 1870 | Date of Death - 22 February 1870 |
| Rev. Bro. Michael A. Murphy OMI | | 1870 | Date of Death - 19 January 1887 |
 | Rev. Bro. ( Fr.) Patrick O Flanagan OMI | | 1870 - 1874 | --- |
| T.W. Mc Mahan Esq | | 1874 - 1875 | |
| Rev. Fr. Patrick O Flanagan OMI | | 1875 - 1880 | Date of Death - 28 January 1889 |
 | Rev. Bro. (Fr.) J.A.R. Smyth(e) OMI | 1st Rector of the (now) College. Opened on 10 January 1881 | 1880 - 1883 | Date of Death - 4 May 1888 |
 | Rev. Fr. Charles H. Lytton OMI | | 1883 - 1885 | Date of Death - 3 December 1924 |
 | Rev. Fr. Jules Collin OMI | | 1885 - 1888 | --- |
 | Rev. Fr. M. Dubreuil OMI | | 1888 - 1889 | Date of Death - 25 November 1912 |
 | Rev. Fr. Patrick Dunne OMI | | 1889 - 1901 | Date of Death - 17 October 1922 |
| Rev. Fr. Jules Collin OMI | | 1901 - 1902 | Date of Death - 9 August 1927 |
 | Rev. Fr. Charles A. Beaud OMI | | 1902 - 1905 | Date of Death - 28 December 1931 |
 | Rev. Fr. Charles S. Matthews OMI | | 1905 - 1921 | --- |
 | Rev. Fr. John A. Guyomar OMI
| Consecrated as Bishop of Jaffna on 16 January 1924 | 1921 - 1924 | Date of Death - 27 February 1956 |
| Rev. Fr. Charles S. Matthews OMI | | 1924 - 1936 | Date of Death - 1 November 1969 |
 | Rev. Fr. Timothy M.F. Long OMI | | 1936 - 1954 | Date of Death - 30 April 1961 |
 | Rev. Fr. S.N. Arulnesan OMI | | 1954 - 1960 | Date of Death - 3 February 2006 |
 | Rev. Fr. P.J. Jeevaratnam OMI | | 1960 - 1966 | Date of Death - 14 March 1985 |
 | Rev. Fr. T.A.J. Mathuranayagam | | 1966 - 1976 | Date of Death - 27 July 2010 |
 | Rev. Fr. John A. Francis OMI | | 1976 - 1979 | Date of Death - 29 January 2002 |
 | Rev. Fr. G.A. Michael (Francis) Joseph | | 1979 - 1992 | Date of Death - Not Known |
 | Rev. Fr. Alphonsus I. Bernard | | 1992 - 2002 | |
 | Rev. Fr. Dr. Justin Gnanapragasam | Consecrated as Bishop of Jaffna on 28 November 2015 | 2002 - 2007 | |
 | Rev. Fr. Jero Selvanayagam | | 2008 - 2018 | |
 | Rev. Fr. Anton P.Thirumahan | | 2018 - Current | |
