The county man, who has not been named, was in the middle of completing the 600-mile cycle ride when the thieves struck.
The bike was taken from outside Stan Jones Cycles, on Wyle Cop, at about 12.15pm on Tuesday after the 35-year-old rider had popped in to buy some parts for repair work.
Detectives from West Mercia Police are now investigating the incident and two 16-year-olds have been arrested on suspicion of theft.
The bike is still missing and an appeal for information to help trace it has been issued by police investigating the crime.
Officers said the fundraiser was only gone 'a few moments' when two youths took the bike, which is worth up to £1,000.
But despite the setback, the victim was still said to be determind to complete the trek and raise money for his chosen charity, Hope House Children's Hospice.
Constable Simon Lewis, the investigating officer, said today: "The owner is anxious to recover the bike so he can continue his journey to Scotland.
"It is a gent's white Cube Aerial racing bike with air brakes worth about £1,000. It was taken from inside the archway to the courtyard at Stan Jones Cycles while he was buying some parts.
"He is doing the ride to raise funds for Hope House on behalf of terminally ill children."
Constable Lewis also appealed for witnesses, in particular, an elderly woman who is believed to have taken a swipe at one of the offenders with her handbag as he made off on the bike up Town Walls. A number of delivery vans were also parked in the area at the time.
The two suspects were taken into custody at Shrewsbury police station and later given bail, with conditions, while further inquiries are carried out.
Anyone with information is urged to call Shrewsbury police station on the non emergency 101 number or Crimestoppers charity on 0800 555 111.