Hughes announced last year that he would step down as chief executive of the dementia care and research charity after 10 years in the role.
Samaritans announced today that Hughes would succeed Ruth Sutherland, who said last year that she would step down in March to pursue a portfolio career after almost five years leading the charity.
Hughes won praise in the sector in 2015 for his robust response to a critical article in The Sun newspaper that claimed 50p of every pound donated to the Alzheimer’s Society was spent on staff wages and pensions.
He said The Sun had missed the point of the charity's work and called on sector leaders to help modernise how the media and the public understood the way charities worked.
Hughes announced his departure from the Alzheimer’s Society in September last year, shortly after a Twitter account purporting to be run by Alzheimer’s Society employees began publishing serious criticisms of the charity’s senior management.
A spokeswoman for the charity said it was "complete coincidence" that the Twitter account was set up a week before Hughes’s departure was publicly announced, adding: "Jeremy’s decision to step down, as is usual for people at this level, has been planned for some time."
Hughes said in a statement today that he felt "enormously privileged" to be appointed to the new role. "Never has the need for Samaritans been greater," he said.
"The dedication and expertise of volunteers and staff are a model many other charities aspire to."
Jenni McCartney, chair of Samaritans, said Hughes would bring a "wealth of experience" from his voluntary sector career.
"Jeremy joins at an exciting time for us and I look forward to working with him to build on our recent successes to ensure that we achieve our mission: fewer people dying by suicide," she said.