Police said it happened near the CTA Blue Line's Damen Avenue stop in the Wicker Park neighborhood just after 6 a.m.
A 52-year-old man on a moving train intentionally lit his belongings on fire, causing burns to his leg, police said.
The fire was extinguished, and the man was taken to Stroger Hospital in good condition, police said.
Earlier Friday, the Chicago Fire Department said the man set himself on fire, adding that he was in critical condition.
CPD's arson detectives and Bureau of Alcohol, Tobacco, Firearms and Explosives special agents responded to the scene.
Police said ATF agents took the man into custody. No other injuries were reported, police said.
"There is no threat to rider safety stemming from this incident," the CTA said.
Longtime CTA passenger Meghan Joost said she was riding the Blue Line when her train came to an abrupt halt on Friday morning.
Joost said a passenger used an onboard intercom to alert the conductor to what CPD called a small fire before the train ultimately came to a stop.
"I've been spit on. I've been harassed. I've been threatened. You know, it gives me severe anxiety," Joost said.
Friday morning's fiery incident happened on the same day CTA officials planned to bolster their police presence at stations and stops across the city after submitting a safety plan earlier this week to the federal government.
"Where were these patrols this morning? In my mind, unless you have someone on each and every CTA train car, there's absolutely no way you can stop this," Joost said.
The plan calls for more police officers, along with additional private security K-9 units.
"I'm going to be honest: I get on certain stops. I see the police are security, and they're just standing around, talking to one another. They are not patrolling," Joost said.
SEE ALSO | Man accused in Blue Line fire attack facing new arson charges in separate blaze at City Hall
This investigation is also unfolding just one month after a man set a woman on fire on a Blue Line train in the Loop and left her with serious injuries. That man is now facing several charges.
Joost says the new CTA safety plan does not make her feel any safer. She says she wants more city leaders to ride the CTA to get a better sense of just how safe some passengers feel.
"You're putting a Band-Aid on a broken leg," Joost said. "I want you to ride with with me on the CTA at 5:30 in the morning, without your security detail, and tell me it is safe, because it is not. And any regular CTA rider will tell you the exact same thing."
Some riders said they noticed the additional officers on-hand.
"I see a lot more police in the area; I feel like that's actually what's helping. But I feel like it's really our mindset. Police can be around, but it's really how you think," CTA rider Jamell Foster said.
The incident caused extensive delays for Blue Line riders.
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