Jamie McDonald posted on his website that a bag containing his wallet and hours of video footage of his cross-Canada journey was returned to an area near where the attack happened early on New Year's Day.
McDonald says there were three attackers and that he reported the incident to police.
He has been running unassisted across Canada east-to-west since March 9th, pushing his belongings in a three-wheeled cart.
The trip is raising money in aid of British and Canadian children's hospital charities.
McDonald says he was shaken up by the attack, but is physically fine.
"I have been amazed at the response, from friends and strangers and from the British and Canadian media, both of which have helped spread my story," McDonald posted on his website on Wednesday.
"I wish the story didn't have to have an unfortunate incident in order to reach people, but I'm glad in a way because the more people that know about my journey, the more children it might be able to help."
McDonald posted on his Twitter account earlier on Tuesday that he was planning to celebrate New Year's Eve at the Earl's restaurant in Banff, noting that his tab was being covered.
He stressed on his website that the attack did not happen at Earl's, but elsewhere later in the evening.
He said he fled quickly, leaving his bag.
"Although I'd been told my bag had been taken, it appears that whoever did so had a change of mind, as the bag was found at/near the place I left after the attack," McDonald said on his website.
McDonald's website says that as a child, he was in and out of hospital for nine years with a rare spinal condition known as syringomyelia, as well as a very weak immune system.
He said the experience hasn't soured his thoughts on Canada.
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