Prosecutor Bernard Carter did not return a message from the Post-Tribune seeking comment, but his spokeswoman, Diane Poulton, said the case was being reviewed.
Detectives met with Deputy Prosecutor Michael Greener on Wednesday and Thursday with statements from victims and other evidence before learning the teen would not be charged.
Both victims, ages 15 and 12, provided similar descriptions of their attacker, who grabbed them both in early morning hours while they waited for their school buses on the east side of the city.
The rapist took each victim into a different vacant building in the Marshalltown/Dorie Miller Housing Development area where he sexually assaulted them.
The older teen, who said she was assaulted repeatedly, reported her rape on Feb. 26. The 12-year-old was assaulted March 6.
One of the victims is a student at Emerson School for Visual and Performing Arts.
Victims reported the assailant had a knife he used to threaten them during the attack. Police recovered knives near the scenes of both incidents.
Police released the teen about 3 p.m. Thursday, 48 hours after his arrest.
The Neighborhood Enforcement Team had been conducting additional patrols in the area earlier this week, but it isn't clear if that increased police presence continues.