In April 2014 Jack Sexty completed the Greater Manchester Marathon on a pogo stick in 16 hours and 24 minutes.
But earlier this month the course was found to be 380m too short and all timings for the 2013, 2014 and 2015 events were declared null and void.
Guinness World Records said the record Mr Sexty set will no longer stand.
"We would invite Jack to go for the record again in the future and we hope this won't deter him from breaking records in the future," a spokesman said.
Mr Sexty, from Bristol, said he "wouldn't be losing any sleep" over the decision.
He said in reality he believed he had done more than a marathon because of having to hop on and off pavements.
"I have video of the event and if Guinness want to watch all 16 odd hours they are more than welcome.
"I still have the record for the most distance bounced in 24 hours. That was the original record I was going for.
"The only reason I had the fastest marathon record is because I'm the only person to have done it."
Marathon courses are measured out using a bicycle fitted with a counter to calculate distance by the turning of the wheels.
The Association of UK Course Measurers (AUKCM) said an accredited measurer had ridden the course in 2013 but indicated there had been an error in the calibration of the bicycle wheel.
The mistake, caused by a measuring error, affected some 24,000 runners who competed in 2013, 2014 and 2015. Their timings are no longer recognised.
A true marathon distance is 26 miles and 385 yards.

Titanic Quarter Ltd has now taken on fresh borrowing of up to Â£75m from Danske Bank.
The Davidson Kempner fund took control of the loans in 2014 as part of a deal with Ulster Bank.
It came at a time when Ulster Bank was working to drastically reduce its property loan book.
Most of those loans were sold to US funds which are generally not intending to build long term relationships with borrowers.
James Eyre, the commercial director of Titanic Quarter, said the refinancing deal with Danske was an important step.
"We are delighted to be back working with a local bank and to have significant additional financial support from the shareholders which reinforces their commitment and confidence in Titanic Quarter," he said.
He suggested that it could mean that work begins on various stalled developments.
"These long-term facilities will optimise Titanic Quarter's strategy to progress further planned developments including Grade A offices, media, hotels, residential, leisure and tourism," he added.
Ciaran McLaughlin, corporate banking manager at Danske Bank, said: "Danske Bank is pleased to have agreed long term facilities with Titanic Quarter on its existing investment assets, which are strategically important to the city.
"It was an easy decision for Danske Bank to get involved given the significance of the project."
A student who bounced his way into the record books has been stripped of the accolade after it emerged a marathon route was too short.
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The firm developing Belfast's Titanic Quarter has repaid loans which were held by a US investment fund.