A child's body, "strongly believed to be that of Mariah Woods" was found in a creek in neighboring Pender County, Onslow County deputies said in a statement.
Mariah was reported missing from her bedroom on Monday, which led to a massive multi-agency search that also included hundreds of volunteers.
An autopsy will be performed to determine the cause of death and to verify the girl's identity, the statement said.
Onslow County deputies and the Federal Bureau of Investigation on Friday arrested Earl Kimrey, 32, who was held on bond of more than $1 million.
Kimrey also faces burglary, felony, larceny and possession of stolen property charges, a statement issued by the FBI and Onslow deputies earlier on Saturday said.
The statement did not say whether Kimrey had obtained a lawyer.
Evidence gathered during the investigation led investigators to believe that Mariah was dead, even before the girl's body was found on Saturday night, they said.
Woods said she put her daughter to bed at around 11 p.m. on Sunday, and said her boyfriend saw the girl about an hour later when the child got up and he had told her to go back to bed, WRAL, an NBC affiliate in Raleigh, North Carolina, reported.
The couple contacted the Onslow County Sheriff's Office early the next morning to say the girl had disappeared, officials said.
A days-long search ensued with hundreds of police officers, military troops and volunteers searching the rural area around the family's mobile home in Jacksonville.
(Reporting by Bernie Woodall in Fort Lauderdale, Fla. and Brendan O'Brien in Milwaukee; editing by Alexander Smith, Stephen Powell and Diane Craft)
(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)