The 22-year-old was forced off early in the second half of the 1-1 draw with Oldham on Friday and looks like he missing out on the trip to face the npower League One leaders.
But manager Kevin MacDonald said the club's medical staff will assess the injury, picked up in a tackle, in the build up to the lunchtime kick-off.
If Thompson misses out then Tottenham loanee Nathan Byrne could get the nod for his first start since making the move from White Hart Lane last week.
Midfielder Tommy Miller missed Friday's game with the Latics with an injury he had been playing with in the Robins' previous matches. He will also be assessed ahead of the match.
Fourth-placed Swindon head to Doncaster knowing victory would lift them to within one point of Brian Flynn's men.