Emery will take over from Sir Paul Ennals, who is leaving his post as the chief of the NCB on 1 August after 13 years in the role.
The TDA director began her career as a primary teacher in Avon and Hampshire before eventually becoming the dean of education and psychology at what is now the University of Worcester.
Emery was an adviser to the Department for Education where she led the integration of local support teams for health, education and social care, before taking up her post at the TDA in 2007.
Dame Gillian Pugh, chair of NCB, said: "Hilary’s rich and varied experience reflects NCB’s commitment to supporting children and young people across a range of settings.
"Her expertise, passion and commitment to the engagement of children and young people equip her excellently for understanding the issues facing NCB’s members, and leading NCB’s diverse work programme."
On her appointment, Emery said: "I am excited at the challenge of leading NCB and taking forward its commitment to using evidence and research to support policy, practice and improvement. I am passionate about making a difference to the lives of children and young people, listening and responding to their needs and interests."
