Carr, who worked with former Blues boss Paul Cook at Sligo Rovers in Ireland, joined the Spireites in the summer of 2013 but on Friday afternoon the club announced that he had left by mutual consent.
“I would like to thank Gerry for his efforts over the last two years and wish him all the best for the future,” said Chesterfield chief executive Chris Turner.
Carr said: “I have thoroughly enjoyed my two years as Chesterfield’s academy manager and feel the club will see the benefits of the work I have done in the forthcoming seasons.
“I feel it is now the right time to pursue other opportunities in the game and I wish Chesterfield good luck for the future.”
Chesterfield said an announcement regarding Carr’s successor will be made in due course.