Law enforcement authorities are conducting an investigation into how exactly the incident unfolded.
Passengers say the man -- identified as Chicago resident Elvis Jackson -- burst past security at the gate and boarded an aircraft Tuesday night.
The 33-year-old suspect has been charged with two misdemeanor trespassing charges and sits in county jail, unable to post the $35,000 bond he was slapped with when he appeared before a judge Wednesday morning.
Witnesses say they saw Jackson allegedly sneak on the Southwest Flight 908, which was headed to Birmingham, Ala. They told the crew, and authorities removed Jackson.
The flight was cleared for takeoff approximately one hour later.
Jackson, who is a nursing assistant, was in bond court Wednesday wearing a white, plastic jumpsuit. His public defender argued he should be released on bond because he has no record and has lived in Chicago with his father for 17 years.
ABC7 Chicago talked to one passenger who witnessed the security breach.
"This gentleman behind me observed the whole thing. He notified the flight attendant, said the person was boarding without a boarding pass, and a few minutes later, boarding stopped and a few minutes after that, police officers showed up on board and escorted this person off," said a passenger who identified himself as Doug.
In his South Side neighborhood, ABC7 spoke to Jackson's brother who cannot believe what has happened.
"That is kind of crazy. I couldn't tell who would be thinking of doing something like that anytime soon,"said Michael Jackson, brother.
Michael Jackson says he doesn't know his brother Elvis very well as they were raised separately. But he knows his brother has taken medication before to treat mental health conditions.
"He doesn't talk that much. He don't even say nothing, he don't explain nothing to nobody, nobody know," he said.
Southwest Airlines referred requests for information to the Chicago police. Chicago aviation commissioner Rosemarie Andolino said, "We're…working with TSA and garnering more information on how that penetration happened, and if it happened. What actually happened, we're looking at that."
At Midway, the security breach is enough to unnerve many passengers flying Southwest Airlines Wednesday.
"You see how tight security is and you see all the problems flying these days, so it would make you nervous that somebody could get through. I still find it hard to believe though," said Dave Berdusco, Southwest passenger.
" I don't know how you can get on a plane without a boarding pass. It has to go through that scanner as you're walking to the plane," traveler Suzanne Shallow said.
It is unclear whether Jackson was already in Midway's gated terminal area after a previous flight or if he got through TSA security without a boarding pass.
There was no word on whether the suspect would face any federal homeland security charges.