Mr Leeks joins from the North of England Refugee Service where he was operations manager. He was formerly a director at the Hong Kong Airport Authority.
CLRL's executive chairman Douglas Oakervee said: 'Clinton is a top class professional who I know will help carry us through the coming phase of the railway, moving towards construction.
'His work on the Hong Kong Airport shows that he knows all about bringing a project in on time and on budget.'
Mr Leeks will take up his new role on July 10.