Shots were fired on the train as it approached the State and Lake station at about 12:09 a.m., police said. A 30-year-old woman was hit in the knee after a verbal confrontation with the shooter.
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The victim was rushed to Northwestern Hospital and her condition has not been made public. She could not tell police any information about the suspect or why the argument started, authorities said. Police are looking for the shooter.
The shooting caused chaotic moments for other CTA passengers. Witnesses said they found out someone had a gun on the train and moved to another car when shots were fired.
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"At that point, everyone was just crammed into one car," said Red Line passenger Carlos Leon.
Red Line trains were rerouted over the Loop and shuttle buses were sent between the Fullerton and State and Lake stations until service resumed, the CTA said in a statement.
The incident marks the fifth shooting on the Red Line so far this year, according to ABC7 data. It is the second Red Line shooting this month.
Chicago police recently announced they had stepped up patrols on the CTA after a father was shot and killed earlier this month.
Some officers from units like gangs and narcotics have been shifted to the CTA. But Chicago Police Supt. David Brown has previously said that because the system is so big, it does not have enough resources to put an officer on every train and bus.
The CTA also announced recently that it is adding new K-9 teams. It will provide up to 100 unarmed guards and 50 canines per day throughout the rail system.