Revd Jonathan Robinson, 73, is accused of abusing the 15-year-old boy in the capital Delhi at a youth hostel.
The boy was from an orphanage that Revd Robinson founded in Vallioor in the south of India, which has now been shut.
Mr Robinson denies the charges, and a submission given on his behalf to court has said that the alleged victim was "threatened and forced" into claiming he abused him.
The vicar was on Interpol's wanted list for four years, however Indian authorities recently took him off in the hope Mr Robinson would voluntarily come forward.
He has been granted bail, and premilinary proceedings continue on Monday.
A full trial is expected early in 2016.
