Embiid's agent, Arn Tellem, said in a statement that the former Kansas star underwent the procedure at Southern California Orthopedic Institute.
The surgeon, Dr. Richard Ferkel, said that Embiid "tolerated the surgery without difficulty" and claimed that the 7-foot center should "be able to return to NBA basketball."
"Two screws were inserted into the navicular bone in Joel Embiid's right foot," Ferkel said in the statement released by Tellem. "The surgery went very well and I'm confident that after appropriate healing he will be able to return to NBA Basketball. Joel tolerated the surgery without difficulty and will begin his rehabilitation in the near future."
Yahoo! Sports earlier reported Embiid's timetable for recovery.
Embiid is not attending Thursday's NBA draft because he can't fly for 10 days to two weeks post-surgery, Tellem said Thursday. Embiid was projected by many to be the first pick before the announcement of the surgery.
A native of Cameroon, Embiid already was dealing with health questions regarding his back, which forced him to miss the Big 12 and NCAA tournaments this past season.
He worked out earlier this month for the Cleveland Cavaliers, who have the No. 1 overall pick in the draft, and sources said he fared well and that the medical testing also came back without much concern.
Embiid also participated in a one-on-none workout in front of NBA teams in Santa Monica, California. He was scheduled to work out for the Milwaukee Bucks, who hold the second overall pick, later this week.
Embiid averaged 11.2 points, 8.1 rebounds and 2.6 blocks this past season as a freshman at Kansas.
If Embiid slips significantly in the draft, he wouldn't be able to recoup the money he'd lose. His total disability insurance policy was purchased through the school, according to Jim Marchiony, an associate athletic director at Kansas.
Marchiony confirmed that the school purchased a $5 million policy, the maximum allowed under the NCAA insurance program, through the NCAA Student-Athlete Opportunity Fund, which allows schools to apply for need-based assistance on behalf of its players.
The policy purchased through the NCAA program does not allow for loss-of-value insurance, a rider attached to insurance policies that permits athletes to collect if they fall far enough in the draft from their projected position at the time they sign the policy. Athletes can get loss-of-value policies, but they have to go outside the NCAA program to do so.
ESPN.com's Jeff Goodman, Andy Katz and Darren Rovell contributed to this report.
How Far Will Embiid Fall?
In light of Joel Embiid's stress fracture in his right foot, Chad Ford discusses where he believes Embiid will go in his latest NBA mock draft, and also talks about where Andrew Wiggins and Jabari Parker will be drafted.