He takes over from Charles Barnett.
Mr Gillespie is the former managing director of Cheltenham racecourse and stepped down last year after 32.
Pony racing has been running in Britain since 2004 and in the past eight years the sport has grown rapidly.
"It is such an exciting time for pony racing with some great initiatives planned," said Clarissa Daly, chief executive of the Pony Racing Authority.
"With Edward's experience, passion and knowledge we really should be able to take the sport to the next level.
"Over 100 graduates from pony racing have already gone on to ride under Rules with many more working within the racing industry; we are aiming to provide many more."
For more information visit: www.ponyracingauthority.co.uk