John Atkinson, who helped lead the ParalympicsGB swimming team to 39 London 2012 medals, has quit his post.
The Briton, who was appointed to the role of national performance director in 2010, will now head Swimming Canada's high-performance programme.
"I have had a successful 12 years across different roles with British Swimming," said Atkinson.
"However, the opportunity to lead the Olympic programme in Canada was too good a challenge to turn down."
Atkinson was considered one of the favourites to fill the national performance director role in Britain vacated by Australian Michael Scott in November.
British Swimming say they will reveal a new appointment for the role, and their new head coach, next week.
The sport's chief executive David Sparkes commented: "We're sorry to be losing John. He's made a massive contribution to British Swimming, both in his time with the swimming programme and latterly by leading the highly successful team to the Paralympics in London.
"We wish him well in Canada and look forward to seeing him in his new role at the next international competition."
National performance director Tim Reddish will lead the disability swimming programme on an interim basis until Atkinson's successor is appointed.