Pereira will return to his home state Goa in order to stay with his family.
"Derrick has been excellent ambassador during his stay at Pune FC. We wish him well for all his success in future endeavors," Head Operations Pune FC, Chirag Tanna said.
"The 51-year-old's departure brings to an end a fantastic spell," he added.
Pereira's last game for Pune FC will be the home game against Pailan Arrows on May 11.
During his stint at Pune FC, the club finished third in I-League 2009-10; fifth in 2010-11 and 2011-12 seasons.
"The team has worked very hard with the focus of finishing the season on a high. The management will announce the new coach shortly," Tanna said.