The Home Office said his role will be to act independently and on behalf of the public to ensure that information on the National Identity Register is accurate and secure.
Pilling, who from 1997 to 2005 was permanent secretary of the Northern Ireland Office, will also be responsible for monitoring the use of identity cards and will report to the home secretary on the way the National Identity Service is operated.
His appointment on 1 October, 2009 will be in time for the issue of the first identity cards to people in Manchester on a voluntary basis, ahead of national rollout.
The identity commissioner will not be responsible for identity cards for foreign nationals, which are subject to oversight by the information commissioner and the chief inspector for UK Border Agency.
Pilling said: "In the early weeks and months as I work out how best to do the job I intend to listen to the people across the National Identity Service and to people outside the system with views about my new role."
Philippe Martin, senior analyst at Kable, said: "This is likely to be a limited role, for two reasons. Firstly, a possible change of government which will mean the scrapping of the identity scheme. Secondly, the likely limited take-up of a non-compulsory scheme."