Cyclist Michael Dougall took to Twitter to voice his anger about the positioning of the bus shelter between Glasgow Green and the city's Velodrome.
Glasgow City Council apologised for the inconvenience and vowed to carry out work to change the route.
The cycle path markings have now been repainted, with the lane routed behind the bus shelter.
The site is in an area of the city which was regenerated for the 2014 Commonwealth Games.
A cycle lane in Glasgow which had a bus stop built in the middle of it has been rerouted.