| SL No. | Director | Period From | Period To |
| 1 | Sri. Jon Ross M.A | 1866 | 1884 |
| 2 | Dr. K Bhaskaran Nair | 1960 February | 1968 August |
| 3 | Prof. V Gopalan Nair | 1968 September | 1970 October |
| 4 | Prof. V Madhava Menon | 1970 November | 1972 March |
| 5 | Dr. Molly Thomas | 1972 April | 1976 March |
| 6 | Prof. T R Subhayyan | 1976 April | 1980 July |
| 7 | Smt. J Lalithambika IAS | 1980 November | 1981 January |
| 8 | Smt. K V Kunjunni Menon IAS | 1981 February | 1981 November |
| 9 | Smt. Lizzy Jacob IAS | 1982 January | 1983 January |
| 10 | Shri. Rudhra Gangadharan IAS | 1983 August | 1985 October |
| 11 | Smt. Sudha Pillai IAS | 1986 June | 1986 August |
| 12 | Shri. K Mohandas IAS | 1986 August | 1987 July |
| 13 | Shri. S Sundareshan IAS | 1987 September | 1988 February |
| 14 | Shri. Thomas C George IAS | 1988 July | 1989 October |
| 15 | Shri.Kuruvilla John IAS | 1989 November | 1991 December |
| 16 | Smt. Neele Gangadharan IAS | 1992 January | 1992 July |
| 17 | Shri. V P Joy IAS | 1992 November | 1996 August |
| 18 | Smt. Lida Jacob IAS | 1992 August | 1996 June |
| 19 | Shri. C K Viswanathan IAS | 1997 June | 1998 May |
| 20 | Shr. L C Goyal IAS | 1998 May | 1999 February |
| 21 | Smt. Lida Jacob IAS | 1999 March | 1999 June |
| 22 | Shri. K Chandrasekhara Babu IAS | 1999 June | 2001 June |
| 23 | Shri. V P Joy IAS | 2001 June | 2001 July |
| 24 | Shri. Raju Narayana Swamy IAS | 2001 July | 2001 August |
| 25 | Shri. C K Viswanathan IAS | 2001 August | 2002 June |
| 26 | Smt. Sarada Muraleedharan IAS | 2002 June | 2003 April |
| 27 | Smt. Tinku Biswal IAS | 2003 May | 2003 May |
| 28 | Dr. Asha Thomas IAS | 2003 June | 2003 October |
| 29 | Shri. B S Mavoji IAS | 2004 February | 2006 January |
| 30 | Shri A Ajithkumar IAS | 2006 January | 2006March |
| 31 | Shri. B S Mavoji IAS (In charge) | 2006 March | 2006 December |
| 32 | Shri V R Padmanabhan IAS | 2006 February | 2008 May |
| 33 | Shri. K Shashidara IAS | 2008 February | 2009 May |
| 34 | Shri. P M Ali Asgar Pasha IAS | 2009 May | 2009July |
| 35 | Shri. K. Gopalakrishna Bhat IAS | 2009 July | 2011 October |
| 36 | Shri. K Ajayakumar IAS | 2011 October | 2013 August |
| 37 | Dr. P.K.Velayudhan | 2013 August | 2014 March |
| 38 | Shri. M Nandakumar IAS | 2014 May | 2016 May |
| 39 | Shri. Sheik Pareeth IAS | 2016 June | 2016 November |
| 40 | Smt. M S Jaya IAS | 2016 December | 2018 March |
| 41 | Smt. Haritha V Kumar IAS | 2018 June | 2019 July |
| 42 | Smt. V. Vigneshwari IAS | 2019 October | 2023 June |
| 43 | Sri. Sudhir K IAS | 2023 June |