The Filmfare Best Director Award is given by the Filmfare magazine as part of its annual Filmfare Awards South for Malayalam films.
| Year | Director | Film | Ref |
|---|---|---|---|
| 2010 | Ranjith | Pranchiyettan & the Saint | [1] |
| 2009 | Hariharan | Pazhassi Raja | [2] |
| 2008 | Ranjith | Thirakkatha | [3] |
| 2007 | Babu Thiruvalla | Thaniye | [4] |
| 2006 | Roshan Andrews | Notebook | [5] |
| 2005 | Blessy | Thanmatra | [6] |
| 2004 | Blessy | Kaazhcha | [7] |
| 2003 | Sathyan Anthikkad | Manassinakkare | [8] |
| 2002 | Lal Jose | Meesa Madhavan | [9] |
| 2001 | Vinayan | Karumadikuttan | [10] |
| 2000 | Jayaraj | Karunam | [11] |
| 1999 | Shyama Prasad | Agnisakshi | [12] |
| 1998 | Sreenivasan | Chinthavishtayaya Shyamala | [13] |
| 1993 | Shaji Kailas | Ekalavyan | [14] |
| 1992 | Sibi Malayil | Sadayam | [15] |
| 1991 | |||
| 1990 | |||
| 1989 | |||
| 1988 | Padmarajan | Aparan | |
| 1987 | Pratap Pothan | Hrithubhedam | |
| 1986 | |||
| 1985 | |||
| 1984 | |||
| 1983 | |||
| 1982 | Balu Mahendra | Olangal | |
| 1981 | K. S. Sethumadhavan | Oppol | |
| 1980 | Bharathan | Chamaram | |
| 1979 | Bharathan | Thakara | |
| 1978 | I. V. Sasi | Yaetta | |
| 1977 | I. V. Sasi | Itha Ivide Vare | |
| 1976 | Sreekumaran Thampi | Mohiniyattom | |
| 1975 | Bharathan | Prayanam | |
| 1974 | K. S. Sethumadhavan | Chattakari | |
| 1973 | K. S. Sethumadhavan | Pani Theeratha Veedu | |
| 1972 | K. S. Sethumadhavan | Punarjanmam |
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