Cardinal Thottunkal was born on June 15, 1959 in Nedungadappally.

He was ordained a Priest on June 11, 1986 for Battery (Bathery) (Syro-Malankarese), India, and on June 18, 2001 he was appointed Auxiliary Bishop of Trivandrum (Syro-Malankarese), India and Titular Bishop of Chaialum. His ordination as Bishop took place on August 15, 2001.

On September 11, 2003 he was appointed Bishop of Tiruvalla (Syro-Malankarese), India, and was installed on October 2, 2003. A few years later, on May 15, 2006, he was appointed Archbishop of Tiruvalla (Syro-Malankarese), India and installed there on June 10 of that year.

On February 8, 2007 he was selected as Major Archbishop of Trivandrum (Syro-Malankarese), India and was confirmed in that role two days later, on Ferbuary 10. He was installed there on March 5, 2007.

He was elevated to Cardinal on November 24, 2012 and appointed Cardinal-Priest of San Gregorio VII.