St. Stephens College was founded in 1964 after the name of St. Stephen, the first martyr of Christianity. The college was the fulfillment of a long cherished desire of its founder, His Grace The Most Rev. Mar Thoma Dionysius. A number of educational institutions testify the deep devotion of the founder to the cause of higher education in and around Kerala and Tamilnadu.
The college was formally declared open by His Holiness Mar Baselios Augen I Catholicos of the East on 8th July 1964. Prof T.C. Joseph, Professor of Botany, Union Christian College, Alwaye, was appointed as the Principal and the Junior College started functioning at Mount Tabor premises, Pathanapuram. In 1968 the College was shifted to its present site, in the serene village of Maloor, 6 kms away from Pathanapuram. The College was upgraded in 1978 and now offers Degree courses in Mathematics, Physics, Chemistry, Botany, Zoology, Economics and Commerce . With the introduction of M.Sc. Course in Zoology in1995, it was upgraded as a Post Graduate College. M.Sc. Course in Chemistry was sanctioned in 1999 and M.Sc. Physics was sanctioned in 2001. Department of Zoology has been recognised as a Research Centre by the University of Kerala in 2000.Students can do research leading to Ph.D here. The college was accredited at the B++ grade by the NAAC Peer Team which visited the institution in 2004