His goal was to play a full 82-game season, but he complained of soreness for the past three days, which prompted the Bulls' medical staff to look into the matter closely and discover the problem.
"I was shooting my shots [to the doctor] to try to maybe find a reason why the MRI showed what it showed," Markkanen said. "I really want to play, but at the same time I had to take a step back to see what's actually smart, so I think they made a good decision and I agreed that it could get worse."
He couldn't recall a specific play or game where the injury happened as he tried to push through pain but was shocked to learn the news.
"We're always gonna look out for the best interest of our guy," Bulls coach Jim Boylen told reporters before Friday's game against Sacramento. "Lauri had a goal to play 82 games and he fought through the oblique and he fought through the ankle. We felt those were things that were acceptable to fight through.
"This is not something that we are gonna have him fight through. He wants to play. He's disappointed that he's not playing and we hope we get him back as soon as possible."
Markkanen, who is averaging 15 points and 6.5 rebounds, was coming off a 21-point performance in Wednesday's 117-110 win over the Minnesota Timberwolves. It was his highest-scoring output in more than two weeks.
"Of course it's always disappointing to sit out. You always want to be out there," Markkanen said.
When Boylen met with Markkanen, he was adamant that he could continue to play as they couldn't pinpoint how it happened. It was discovered during the MRI, which was conducted Thursday.
"Lauri never said he wasn't going to play until we met with the doctors and we all said this is the best for him not to play," Boylen said. "I can't tell you how much we appreciate the fact that he's fought through stuff and he wanted to fight through this, but this is not what we were going to do."
Markkanen plans to follow orders from the team's medical staff over the next couple of weeks until he begins rehabilitation.
"I'm going to do whatever they tell me to do, but I think that's the plan to kind of calm down a little bit and then start working my way back up," Markkanen said. "I haven't got that far yet."
ESPN's Eric Woodyard and The Associated Press contributed to this report.