Archibald won gold in the individual pursuit and silver in the points race at the 2018 Commonwealth Games in Australia. She also has four rainbow jerseys at the Track World Championships.
She was included in Team Scotland's squad for the July 28 - August 8 Games, but last month injured both her ankles after she was hit by a car. The 28-year-old also broke her collarbone and suffered a concussion at a World Cup event in May.
"I took two weeks off in January this year while recovering from shoulder surgery. That was a scheduled break," Archibald said in a statement.
"However since then I've managed to fit in, unscheduled: a back fracture, covid, a concussion, a broken collarbone, another surgery, and (the final cherry on top) two sprained ankles and a big ballooned leg.
"I've tried my hardest to keep my head up... but I'm just not coping. So with a very heavy heart I've decided to withdraw from the Birmingham Commonwealth Games."
Archibald's withdrawal will come as a big blow to Scotland, who won their most medals (10) in cycling at the 2018 Games.
Anna Shackley, who was part of the delayed Olympic Games squad for Great Britain last year, is one member of the squad that Scotland will be hoping can pick up a medal in Birmingham.