The Archdiocese of Chicago sent a letter to parishioners Saturday, informing them of the allegation and investigation, which came while the priest was overseas on military duty.
Father Paul Guzman serves at Most Holy Redeemer Parish.
The accusation allegedly happened 25 years before he entered the Mundelein Seminary to prepare for the priesthood, the Archdiocese said.
Cardinal Blase Cupich has asked Guzman to step aside from ministry and live away from the parish, and said Fr. Guzman agreed.
"It is important to remind everyone that, while the Archdiocese takes every allegation of child sexual abuse seriously, the fact of an allegation does not presume guilt," Cupich said. "We should reserve judgement until the investigation is complete and the Independent Review Board makes its recommendation to me."
The allegation has been reported to the Illinois Department of Children and Family Services (DCFS) and the Cook County State's Attorney.