Lawrence Reed, 50, was indicted Wednesday in the CTA fire incident and in an alleged blaze at Chicago City Hall three days before that attack.
The charges in the indictment are punishable by a maximum sentence of life in federal prison.
Reed is being held in custody, pending future court appearances.
Reed has also been accused of trying to sexually assault a female CTA rider, and then attacking a man who intervened in March.
Reed is accused of dousing a woman in gasoline and setting her on fire on a Blue Line train Nov. 17.
She remains in the hospital with critical injuries.
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Reed has a lengthy criminal history, including over 70 arrests.
He's next due in court for the most recent indictment Jan. 20.
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