The company has pledged to raise £100,000 for the organisation with the help of its employees who will take part in a raft of fundraising activities this year.
Among their efforts, staff will take on challenges including the Three Peaks Challenge and the Ride London cycle race.
Flight Centre said it will match all money raised by its team.
The agency chain added that it decided to support Mind after the charity was chosen during a vote among its staff.
The partnership will sit alongside Flight Centre’s own foundation, which was created to provide education to disadvantaged children in South Africa.
Flight Centre’s previous charity was the Alzheimer’s Society for which it managed to raise £240,000 during a two-year partnership.
Will Leonelli, HR director at Flight Centre, said: “Thanks to Mind’s campaigning over the last few years we know that one in four of us will experience a mental health problem each year. Within Flight Centre we want to change attitudes towards mental health and wellbeing in the workplace.
“By working with Mind, we will help this life-changing charity to ensure no-one has to face a mental health problem alone.
“Our fundraising will support the charity’s national helpline, which offers a lifeline to those in desperate need. We will also fund mental health projects both across the UK and within Flight Centre itself to help raise awareness, offer support and change attitudes towards mental health.”
Kathleen Miles, director of fundraising at Mind, added: “We are hugely grateful to the staff at Flight Centre for choosing Mind as their charity of the year and helping to ensure we can support the one in four people who experience a mental health problem in any given year.
“Money raised over the course of this partnership will allow us to continue to be there for people who need it, when they need it the most and to fight to make sure that everyone with a mental health problem gets the support and respect they deserve.”