Mr Harris, 21, allegedly enticed an underage boy to produce sexually explicit videos and photos of himself, the US attorney's office said.
According to court records, Mr Harris admitted to soliciting and receiving explicit images from the minor.
But a spokesperson for the star has denied the allegations.
Mr Harris was arrested on Thursday morning and later appeared in court in Chicago.
He did not enter a plea. A judge said a hearing would be held on Monday to determine if he will stay in custody or be released on bail, according to US media reports.
Mr Harris featured prominently in the popular series Cheer, which followed a cheerleading team from Navarro College in Texas as they sought a national title.
Mr Harris is accused of soliciting images from the minor from December 2018 to March 2020.
The victim informed Mr Harris during their initial online encounter that he was 13 years old, a criminal complaint says.
If convicted on the federal child pornography charge, Mr Harris faces up to 30 years in prison.
The charge comes after a lawsuit was filed earlier this week, in which Mr Harris was accused of child sexual exploitation and abuse of two alleged male victims.
A spokesperson told CNN at the time that "we categorically dispute the claims" and "are confident that when the investigation is completed the true facts will be revealed".
But court documents say Mr Harris admitted during an interview with law enforcement officials to soliciting and receiving explicit images from one of the minors and "at least between 10 to 15 other individuals he knew were minors".
Officials say investigations are ongoing and have called for anyone with more information to come forward.
Cheer was an instant success when it was released on streaming service Netflix in January, and recently won two Emmy Awards.
Mr Harris gained popularity for his enthusiastic "mat talk" - when cheerleaders on the sidelines shout encouragement to teammates during difficult stunts.
Earlier this year, he interviewed celebrities on the Oscars red carpet for The Ellen DeGeneres Show.