The GATE percentile is calculated as follows:

P = ( (N- your rank)/ N) x 100

Where P is percentile and N is total number of candidates appeared for exam.
(N- Your rank) indicates the number of candidates who have scored less marks than you.

For example, if total number of candidates are 100 and 90 of them have less marks than you P = (09/100)X100 = 0.9×100 = 90 percentile.

For another example: A guy form Mechanical Engineering have All India Rank (AIR) 99 and total number of student of students appeared for GATE in Mechanical Engineering are 59338 in 2010. Then his percentile would be calculated as

P = ((59338-99)/ 59338) X 100
= (59239/59338) X 100
= (0.9983) X 100
= 99.83
The candidate has 99.83 percentile.