Marcella Jean Lee, 56, was detained on Thursday about 100 miles (160km) south of Goldsboro, where her mum's remains were discovered.
She faces a felony charge of failure to report a death, according to police.
Police had been searching for Ms Lee for more than three months after a neighbour discovered the body of Arma Roush, 75, inside the freezer.
A post-mortem examination showed no signs of foul play in Ms Roush's death.
A neighbour bought the freezer for $30 (Â£23).
Ms Lee told the buyer not to open the appliance, which was taped shut.
She told the neighbour that members of a local church would come by to collect the contents of the freezer, which she referred to as a time capsule.
A few weeks later in May, the neighbour opened the freezer and found the body.
Ms Lee's mother had been living with her and was last seen in August 2015.
North Carolina police have arrested a woman after her mother's body was found inside a freezer sold at a yard sale.