The 51-year-old, who wanted to stay close to his family, decided to join his former club where he played for eight years as a defender, and is looking forward to bring back past glory when he takes over the side after May 12.
The deal was signed yesterday.
Pereira said that the club was already having trials for the next season, and though the club staff would choose some of the players, he would have the final say.
Pereira's started his coaching career at Vasco where he trained the club for five years till 2005. He later moved to Mahindra United and coached them for four years before moving on to Pune FC.
During his stint at Pune FC, the club finished third in I-League 2009-10; fifth in 2010-11 and 2011-12 seasons. The club is currently placed at the second spot behind Churchill Brothers, in the 2012-13 season.