A youth minister seduced a 12-year-old and had sex with her for nearly two years before he was arrested, prosecutors said yesterday.

Cops picked up Jeremy Fulton, 27, in Maryland last week after he fled, fearing that police had been tipped off about his sickening alleged relationship with a girl that he mentored at Henry Street’s Mariner’s Temple Baptist Church, Assistant District Attorney Kevin Wilson said in Manhattan Criminal Court.

Fulton is facing 25 years to life in prison on charges including rape and sexual assault against a minor. He was arraigned yesterday and held without bail.