The double Stirling Prize winner has been brought on to the heritage watchdog's decision-making committee to replace Piers Gough of CZWG Architects.
Wilkinson said: 'EH performs a really important role in the protection of our built heritage, especially when faced with the pressures of from development.'
He added: 'I am a Modernist at heart, but it must always be subject to its context. The quality of our built environment will always be improved by the skilful interplay of the young and old - as a practising architect it will enable me to offer the right balance of ideas.'
Wilkinson's practice has received international acclaim, and picked up the RIBA Stirling Prize in 2001 for the Magna Centre in Rotherham and in 2002 for the Gateshead Millennium Bridge.
The practice is currently in the running for the 2012 London Olympics Velo Park, with the result of a competition to be announced later this summer, and is shortlisted in the competition to redesign Governors Island in New York.
Wilkinson's tenure with EH will run for the next four years, officially ending on 8 July 2011.