The experienced right-back limped out of the final pre-season friendly of the summer against Hull City last weekend with a foot problem which has left him 50/50 to start at the ‘Jonny-Rocks’ Stadium.
Thompson’s absence would cause some Posh re-thinking as potential replacement Joe Ward has only just resumed training after a 10-game spell on the sidelines.
Teenage right-back Benjamin Mensah has yet to make a first-team appearances which could mean centre-back Josh Knight filling in on the right of the defence, if manager Grant McCann deploys a 4-3-3 formation.
On-loan goalkeeper Harvey Cartwright is also a 50/50 shot to be in the squad because of a thigh problem. If he misses out youngsters Will Blackmore and Will Lakin will battle it out be on the substitutes’ bench.
Darren Ferguson says Peterborough United lacked the ambition to stay in the Championship and he's staying patient while waiting for the right job opportunity to come along
Supercomputer predicts likely outcome for Plymouth Argyle v Peterborough United, Derby County v Barnsley, Sheffield Wednesday v Charlton Athletic, Bristol Rovers v Oxford United and every other League One fixture
Peterborough United linked with Ben Garrity as Port Vale boss seeks to play down link
Peterborough United should change their winning League One team!
Strong EFL Cup performance has given Peterborough United boss Grant McCann decisions to make ahead of Plymouth rematch
“Nathan just landed funny on his foot in the Hull game,” McCann explained. “It was swollen the next day. He has been back out on the grass training, but he’s 50-50 to play. It could be we lose him for one game so he’s ready for the next 45. It’s the same with Harvey.
"We have options. Benji has done well pre-season and Josh can play there, but we are not writing Nathan or Joe off just yet.”
McCann accepts there will be disappointed players in his promotion-seeking squad who don’t start at Cheltenham. The likes of striker Jack Marriott and summer signing Ben Thompson could well be on the bench.
"We have a really good dressing room,” McCann added. “It’s not going to be just about the 11 who play on Saturday. it will be about all of them over a whole season and the players know that.
"Those who don’t play will keep their focus and be ready when needed. We are lucky to have the best two strikers in League One in Jonson Clarke-Harris and Jack Marriott. Other clubs will disagree, but that's what I feel.
"Pre-season has gone well, but tomorrow we will need to get our gameplan right and follow it. We must make sure we get it right defensively and do our own jobs first. Any game in League One is difficult, especially away from home.
“We need to stay calm throughout the season. There will be times when it seems like a roller-coaster and results don't go our way, but it’s a long season and the focus is on one thing.”
Posh Under 21s have a friendly at Spalding United tonight (Friday, 7pm kick-off).