Embiid was born in Yaounde, Cameroon, to military officer Thomas Embiid and his wife, Christine. He had originally planned to play professional volleyball in Europe but started playing basketball at the age of fifteen, modeling his game after NBA Hall of Fame center Hakeem Olajuwon. Embiid was discovered at a basketball camp by Luc Mbah a Moute, a fellow native of Yaounde and an NBA player. With Mbah a Moute serving as mentor, Embiid moved to the United States at the age of sixteen to devote himself to becoming a professional basketball player.

Embiid enrolled at Montverde Academy, Mbah a Moute’s alma mater, but transferred after his first year due to a lack of playing time. Embiid then attended The Rock School, a Christian academy, in Gainesville, Florida. As a senior he led the team to a 33-4 record and state championship, by averaging 13.0 points, 9.7 rebounds and 1.9 blocks per game.

He was a five-star recruit according to Rivals and committed to Kansas in November 2012.