He replaces Julia Unwin, who left the position in September to take on the role of director at the Joseph Rowntree Foundation.
Reynolds has been a board member of the FSA since May 2006. He has worked as a self-employed consultant advising venture capital houses on business planning for acquisitions and turnarounds in the health and social care markets since 1998.
"I am delighted Ian is joining us as deputy chair," said Dame Deirdre Hutton, chair of the FSA. "His scientific and business background will be an invaluable asset to the agency and his wise council, already in evidence from his time on the board, is a tremendous help to us all."
Reynolds added: "Food issues are at the top of the nation's agenda and I am very impressed by the work the Food Standards Agency has done on food safety and nutrition."