The Supreme Council of the college which includes members of Church of North India (CNI) and Thampu himself, today selected Varghese for the top post.
"In total, three applications were received for the position which was advertised months back. We interviewed the candidates today and the council unanimously decided to appoint Varghese to the post," Alwan Masih, CNI General Secretary told PTI.
Varghese, who was a professor at St Stephen's English department before joining EFLU, will take charge as 13th principal of the college on March 1.
The college had to advertise twice for the post as limited applications were received.
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"First time, we received only two applications. We advertised again but only three people came forward. I asked some of the outstanding alumni too but everybody was reluctant to apply considering the "controversial" nature of the post," Thampu said.
Thampu who studied at St Stephen's and later served the college as a lecturer and officiating principal, took over as the college principal in 2008 and will retire from the post on February 29.