Dundee United have warned fans that some of their big-name players are likely to leave the club this summer.
"We will have some difficult decisions to make for next season," Thompson said.
"We have a lot of guys out of contract and have been trying to re-sign a number of them.
"Some of the younger ones have signed but the senior ones have not.
"It's a case of either what they're looking for is too much or they're not keen to sign again."
Thompson also said that manager Peter Houston, who led the club to this season's Scottish Cup, will have a cut budget for the 2011/12 campaign.
"Peter's already looking for new players for next season so I would expect to see a few changes in the summer," he added.
"That's what happens on the back of having a good season.
"If you look at any team outside the Old Firm who's won anything that team is generally broken two seasons later.
"The good thing from our point of view is that the younger ones are all signed up and we have high hopes for them.
"It will be harder but we will still have a group of very good players.
"We have a budget for next season and Peter knows the limitations.
"It will be reduced from this season but that is for the long-term benefit of the club."