Zachary Todd Anderson, 26, of Monticello, was being held in the Crow Wing County Jail in the death of Alayna Ertl, whose mother discovered her missing from her home in the central Minnesota town of Watkins about 8 a.m.
She was last seen about 2 a.m.
Her body was found nine hours later in a wooded area near Motley in Cass County, about 80 miles to the north.
"Our suspect in this case is a family friend, co-worker of the victim's father, and was staying the night up in Watkins last night," Meeker County Sheriff Brian Cruze said Saturday night.
"He had previously been to that residence and spent a night here and there -- so he's not a stranger and not new to the residence, but was just there for the night." Investigators have not disclosed how the girl died.