A proposal to close the service in the city faced a public outcry when it was announced by the charity last month.
Following a consultation period however, the NSPCC has announced it will retain the service in Derry, however the service in the Craigavon base will end and a number of roles will be made redundant.
NSPCC Assistant Director for Northern Ireland, Bronagh Muldoon, said: “Our mission is to prevent child abuse and we’re making changes to the way we run some of our local services to help us reach even more communities in Northern Ireland.
“Work with schools, including a named person to liaise closely with each and every one, specialist direct services, local campaigns and community partnerships across the country will all be coordinated from a hub, with staff based across two locations, in Belfast and Foyle.”
She added: “We believe we can have the greatest impact with the funding we have by trying to prevent abuse and neglect before it happens.
“These changes would help us achieve that aim in Northern Ireland.”
The charity said it is doing all it can to support the staff affected by the changes, including training and redeployment.
SDLP MLA Mark H Durkan has welcomed the decision to retain the service within Foyle and said it will be a relief to the many vulnerable young children and their families who avail of it.
“The service provided by this programme is key to helping some of our most vulnerable young people deal with their experience of abuse and put them on the pathway to recovery. Given the rise in child sex abuse during the coronavirus pandemic, this service will play a significant role in the months ahead,” he said.