NCT’s last permanent chief executive, Belinda Phipps, left last year after 15 years in the role and was succeeded on an interim basis by Susie Parsons in December. Parsons will return to her interim management consultancy, Lasting Transformations, when Wilkie arrives.
The London-based parent charity the NCT had an income of £17.6m in the year to 31 March 2014, according to the Charity Commission.
Wilkie has 17 years of experience in the voluntary sector, including six years as chief executive of the youth organisation London Youth and five years leading sustainable funding at the National Council for Voluntary Organisations.
He was also one of eight people appointed to the Panel on the Independence of the Voluntary Sector in 2011.
Beryl Hobson, chair of the NCT, said: "Nick has an impressive track record of making a difference for families, and the board is looking forward to working with him to expand our work in supporting every parent across the UK."