The 7-foot forward missed the final two weeks of the season. Chicago finished its season Wednesday with a 22-60 record.
Markkanen was removed from a game against the Raptors in Toronto on March 26 due to extreme fatigue and an accelerated heart rate.
The team says doctors at Rush and Johns Hopkins determined dehydration and nutrient deficiency caused the issues.
This season, Markkanen averaged 18.7 points and 9.0 rebounds per game.
Markkanen will head to Finland to begin his normal offseason program, and then return mid-summer to Chicago to train with Bulls staff.