[1][2][3][4] Varghese was born on 7 February 1953 at Malapallipuram, Kerala, India.

[1][5] He acquired his Master of Theology from Pontifical Seminary, Aluva, Kerala, India and also completed his Master of Arts specialising in History from University of Mysore.

He acquired his doctorate in canon law from Pontifical Urban University, Rome.

[6] He joined St. Joseph's Seminary, Mangalore in 1971 for the diocese of Calicut.

He was ordained a priest by Bishop Maxwell Noronha on 2 April 1981 in Mother of God Cathedral, Calicut.