Prosecutors said the Rev. Bryan Kuchar confessed to the 1995 incident, which allegedly occurred while he was an associate pastor at Assumption Catholic in suburban St. Louis, his first assignment following his 1993 ordination.
For the last year, Kuchar, 36, has been the St. Louis' archdiocese's chief recruiter of young men to the priesthood.
"This came as a devastating shock," Archbishop Justin Rigali said in a statement. "There has been, until now, no such allegation against Father Kuchar."
Rigali encouraged Kuchar to continue cooperating with authorities.
David Clohessy, the founder and national director of the Survivors Network of those Abused by Priests, said priests who commit sexual abuse "are masterful at deceit and deception and that's why they are able to attract these children" and keep their actions secret.
The alleged victim disclosed what happened to his parents and a counselor some time ago but the allegations were not turned over to police until recently.