Brookes, who trained as an economist, left NPC in 2011 to join the hedge fund Fulcrum Asset Management.
He spent 10 years with NPC, joining in 2001 as head of research before becoming chief executive seven years later. He will take up his post at the Paul Hamlyn Foundation on 10 June.
Brookes is also chair of Pro Bono Economics, which he co-founded in 2009 to match volunteer economists with charities that want to address issues relating to measurement, results and impact.
"I am extremely pleased to join the foundation," he said. "As a grant recipient in the past, I know the foundation is a thoughtful and strategic funder, thanks to the tremendous work of Robert Dufton, the board and staff. It is a great privilege to be asked to join such a strong team."
The foundation was established in 1987 by the publisher and philanthropist Paul Hamlyn and is one of the UK’s largest grant-makers, worth £559.6m at the end of 2011/12.
Jane Hamlyn, chair of the foundation and Paul’s daughter, said: "I am delighted that Martin will be joining us as director. His experience in policy, research and impact in the charitable sector and his understanding of philanthropy are ideally suited to our work at the foundation."