The school granted the 6'9" Nigerian permission to pursue transfer opportunities with other NCAA member institutions, but the rising senior will have to sit out a year per NCAA transfer rules.
Obekpa averaged 5.8 points and 27.3 minutes per game during the 2014–15 season. He was second on the team in rebounds per game, with 7.0 per game.
"It was a great three years of growing here at St. John's," Obekpa said in a statement, according to RumbleInTheGarden.com.
"I am forever grateful for the friends and family I have met during my time here. Much gratitude goes out to my coaches, teammates, professors and administrators for all the love and support over the past three years."
He was suspended for two weeks this past March on the NCAA tournament's "Selection Sunday" for failing a drug test, and missed the team's opening round tournament loss to San Diego State.
With the announcement, Obekpa becomes the 10th member of the 2014–15 team that will not return this coming season.
In addition to Obekpa leaving, forward Sir'Dominc Pointer, star guard D'Angelo Harrison, swingman Khdaim N'Diyae, shooting guard Phil Greene IV and Jamal Branch each graduated in May.
The team will also lose brothers Adonis and Joey De La Rosa, as well as guard Myles Stewart, who opted to transfer out of the program as well following the arrival of new head coach Chris Mullin.
Mullin has brought in seven new players to the program - six of whom are immediately eligible - in roughly two months on the job.
But Obekpa's departure could nonetheless pose a significant rebounding challenge for a team that finished 306th in rebound margin last season.