The man, identified by his surname, Ko, was taken into custody in Naju Friday after allegedly abducting the first-grader early Thursday, Yonhap News Agency reported.
Ko, 23, allegedly confessed to the crime, police said.
"[I was] out of my mind after drinking. [I] committed the crime under the influence of liquor," Ko was quoted by police as saying.
Police said Ko lived very close to the victim, who he abandoned on a remote riverside after the alleged rape.
The victim was hospitalized for treatment of injuries to her genitals and intestines.