Francis Benali, who made more than 300 appearances for Southampton FC, ran a marathon and cycled 75 miles (120km) each day for a fortnight in October.
The city council unanimously approved a motion giving him honorary freedom of the city at a special meeting earlier.
Benali, 47, described receiving the honour as "a complete surprise".
"It's just wonderful to be thought of," he added.
The honour was awarded in recognition of Benali's fund raising achievements for charitable causes, as well those as a player and coach at Saints, the authority said.
It confers no rights or privileges, such as driving sheep through the city, and is "purely ceremonial", it added.
The 1,000-mile (1,600km) route linking 44 football clubs took him to south Wales, the Midlands and the North-West, before crossing the country and returning via East Anglia and London.
He raised more than Â£390,000 for Cancer Research.
Benali received a standing ovation from fans when he arrived at St Mary's Stadium at half-time during a home match against Burnley on 16 October.
It followed another challenge in 2014 which saw him running between 20 Premier League stadiums and raising more than Â£265,000 for charity.
As a result he was presented with the Barclays Spirit of the Game award in December 2014, acknowledged as the Cancer Research UK Flame of Hope Award Winner 2015, Fundraising Volunteer of the Year and also the Just Giving Celebrity Fundraiser of the Year 2015.
Other individuals to have been given the honour in Southampton include former Saints managers Ted Bates and Lawrie McMenemy, former player Matthew Le Tissier, and World War One prime minister David Lloyd George.

The "once-in-a-lifetime" opportunity has attracted applications from more than 226,000 people.
The random selection process to choose the 50,000 successful entrants is now under way with the winners being chosen by computer.
People will know by 13 July. The Queensferry Crossing Experience takes place on 2 and 3 September.
The vast majority (97%) of entrants have Scottish addresses with 51% hailing from postcodes near the bridge.
About 5,180 people entered have postcodes from elsewhere in the UK and the remaining 437 are from the rest of the world, including the United States, India and one single entrant from Slovakia.
Economy Secretary Keith Brown said: "We're delighted with the response to the Queensferry Crossing Experience, it really proves just how strongly the new bridge has captured the imagination of the public in the past decade of consultation, development and construction.
"The process to randomly select the lucky 50,000 is now under way and we would ask everyone who has entered to keep their eyes on their email inboxes as, if selected, you only have 48 hours to confirm your attendance.
"It is also pleasing to see the large amount of ballot entries hailing from local postcodes which should ensure local communities are well represented over the weekend.
"To have a walking event of this scale is fantastic for all those successful in the ballot, providing a close-up view of the impressive new crossing and a unique way for people to be physically active."
A former Southampton footballer who ran and cycled to every Premier League and Championship stadium in two weeks has been granted the freedom of the city.
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The online ballot to select 50,000 people to walk across the new Queensferry Crossing has now closed.