[1][2] Lee attended Deer Valley High School in Antioch, California, where he was a starter on the varsity basketball team.

He led Deer Valley to the 2013 CIF North Coast Sectionals to defeat De La Salle High School from Concord, California.

He played in the 2013 McDonald's All American and Jordan Brand Classic games and was named 3rd team USA Today and first-team Parade All-American.

When Cauley-Stein suffered an injury against arch-rival Louisville in the Sweet 16 of the 2014 NCAA Tournament, Marcus Lee stepped up in the following game vs. the Michigan Wolverines in the Elite 8 and scored 10 points, grabbed 8 rebounds (7 offensive), and had two blocked shots, all while committing zero fouls or turnovers.

[4] On April 18, 2014, Lee announced he would return to the University of Kentucky for his sophomore year to join a front court including Cauley-Stein, Johnson, Alex Poythress, Karl-Anthony Towns, Trey Lyles, and Derek Willis.

After short preseason stints with Aris Thessaloniki in Greece[13] and Bnei Herzliya in Israel,[14][15] Lee re-joined the Skyforce for the 2019–20 season.

[17] On August 9, 2020, Lee signed with Vanoli Cremona of the Italian Lega Basket Serie A (LBA) for the 2020–21 season.

[21] In November 2022, he left Manresa and signed with Melbourne United in Australia for the rest of the 2022–23 NBL season.