Leethen Bartholomew's appointment comes as the centre - run by Barnardo's in partnership with the Local Government Association - expands its remit to include preventing child abuse linked to faith or belief, and breast ironing or flattening.
Bartholomew, who has been a social worker for almost 20 years, has spent more than a decade tackling FGM and had spent time training social workers at the national FGM centre prior to its opening in March 2015.
He is due to take over from interim head Meg Fassam-Wright on 4 December. Former head of the centre Celia Jeffreys left the centre at the end of March to become safeguarding children lead at the Barnet, Enfield and Haringey Mental Health NHS Trust.
"I want the centre to not only be known for combating female genital mutilation but also for protecting children from other forms of harmful practices," Bartholomew said.
"I want it to be the go-to place when professionals need research, when they need training and consultancy, in addition to working innovatively with local authorities."
"People are sometimes surprised to find a man so strongly involved in this work, but it's rarely been an issue in the decade I've spent working with affected communities to prevent and tackle FGM.
"The government's aim is to end FGM [in the UK] by 2030, in a generation, and I want us to be able to look back and say the centre played a really active and important role in making that difference.
"I'm just glad to be part of the process and making history."
The National FGM Centre was established to try to prevent FGM through innovative social work, and training professionals like social workers and teachers to spot girls at risk of FGM and to know what to do.
Staff will receive training to adopt a similar approach to prevent child abuse linked to faith or belief, and breast ironing and flattening.
Director of the National FGM Centre, Michelle Lee-Izu said Bartholomew's skills and knowledge in the children's social care sector will complement the centre's highly experienced female specialist team that works directly with women and girls to end FGM.
"It is important men have a role in raising awareness around this serious form of child abuse and preventing new cases of FGM, as well as stopping other forms of harmful traditional practices," she said.
"We welcome Leethen's expert insight in helping the centre to reach out to as many communities as possible to identify and protect children at risk."
Earlier this year CYP Now revealed that the future of the centre was in doubt, but in July the Department for Education announced that the centre would receive more money from its innovation fund for it to remain open.
