Gurnee police responded to the park after receiving 911 calls around 7:50 p.m.
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Police said a white sedan entered the parking lot and drove toward the front entrance, where the suspects got out and started shooting at another person in the parking lot.
The suspects then got out and drove away, police said.
Two people were shot and taken to Advocate Condell in Libertyville with non-life-threatening injuries. A 17-year-old boy from Aurora was wounded in the upper leg and a 19-year-old woman from Appleton, Wisconsin was wounded in the lower leg.
A third person injured their shoulder but declined transport to a hospital.
Both people who suffered gunshot wounds have been released from the hospital as of Monday afternoon.
Video posted on social media showed sheer panic as people ran from the gunfire and people could be seen huddling together inside the park.
"As we were walking by the gate, they started escorting people out, rushing people out toward the front," witness Olga Davil said. "Cops had already surrounded the place. There were two individuals that got shot and we saw blood by the entrance.
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"They did a great job on their part getting everybody else safely," Amy Perez, from Holland, Michigan, said. "It's just sad. It's sad that it keeps happening."
Park security and officers from the on-site Gurnee Police Department Substation responded immediately, park officials said.
Police believe the shooting stemmed from an argument that appears to have begun elsewhere and spilled over inside the Six Flags parking lot, when the occupants of a white sedan pulled up, got out and started firing at someone else. Then they got back into their car and fled.
"Based on the initial investigation, a white sedan entered the Six Flags parking lot and drove toward the front entrance of the park," Gurnee police spokesperson Shawn Gaylor. "Suspects exited the vehicle and began shooting toward another individual in the parking lot. The suspects got back into the white sedan and quickly left the area."
Police said while the shooting appeared to be targeted, the two people injured were not together and it was not clear if either of them was the intended target of the shooting.
People from out of town didn't choose to cancel their plans Monday to come to the park.
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"We were a little hesitant especially with taking children," Susie Sirianni from Streator said. "But I feel like they have good security here, so we feel safe."
"Our family travels to different amusement parks each summer just as a family trip and this is one that we have not been to yet," Perez said. "We still wanted to come down and make the best of it and enjoy the day."
The suspects are not in custody. Police said the shooting was not random and appeared to be targeted.
Six Flags released a statement saying, "Six Flags dedicates our greatest amount of time, talent and resources to safety and security.
"Layers of preventative measures both inside and outside the park are in place for the protection of guests and team members. We continue to review and enhance our protocol on a daily basis to ensure we are providing the highest level of safety.
"Cameras placed in the parking lot and inside the park, uniformed and plain clothes patrols throughout the property, and advanced screening technology allow us to react quickly and provide important information. The park security team is joined by the Gurnee Police Department, who operates a substation at the park."