Phil Hammond was targeted as he ran through Burton-on-Trent, Staffordshire at about 6.30pm on Monday August 2.
Staffordshire Police confirmed that they were called the following day about the robbery, which happened along a path adjacent to a canal in Barton-under-Needwood village.
The offender reportedly threatened the victim with a fruit knife and demanded he empty his pockets.
Mr Hammond was unharmed but the attacker ran off in direction of Stretton with £40 in cash.
Mr Hammond is aiming to run 1,200 miles in 37 days, heading from Leeds to Lands' End, then from Lands' End to Carlisle, and finally back to Leeds.
He spent the night in safety with the family of one a volunteer from The Veteran's Charity.
Mr Hammond, who works for the NHS as a Porter Technician within a medical education team, was shaken after the incident but undeterred in his efforts to raise money, according to The Veteran's Charity.
CEO of The Veterans Charity, Danny Greeno, said "We are shocked and saddened to learn that Phil was mugged yesterday evening during his run and we are very thankful that he was unharmed.
"One of our trustees, who is highly experienced in personal safety, has given Phil some additional advice and our team have arranged to meet up with him at regular intervals throughout his run as well as operating daily check-ins.
"Phil is also carrying a tracker so we can monitor his progress.
"We are very relieved that Phil is OK after this ordeal."
Well-wishers have been boosting Mr Hammond's fundraising total via his JustGiving page.
He has raised almost £2,000 for the charity.
Staffordshire Police confirmed that the job has been transferred to Derbyshire Police.
Anyone with information can contact them quoting log 257 of 03/08.
The offender is described as wearing a blue face mask, blue jacket with the hood up, black jogging bottoms and black trainers.