The Hearts players were criticised last year for their poor levels of fitness and that is something that Jefferies has worked on since his arrival from Kilmarnock at the end of January.
Tynecastle right-back Thomson expects his manager, who is known to be a stickler for fitness, to put them through the wringer when they report back for the start of pre-season training in just over a week's time.
And he revealed that the club's locally-based players have been encouraged to keep themselves ticking over with training sessions at Meadowbank, run by former Hearts midfielder Gary Mackay.
Thomson said: "When the manager first came to the club, I think that he knew straight away that we weren't fit enough.
"He said as much to us in his first few days and said that he would make sure that we were fitter than ever in pre- season.
"Pre-season this year is going to be pretty hard but quite a few of the boys have kept themselves ticking over by going down to Meadowbank and working with Gary Mackay on a Monday, Wednesday and Friday.
"It's been good to keep fit because I think that we will need it for our pre-season, to be honest.
"Gary and Bert Logan have been absolutely brilliant with us and, as well as the general fitness work, they took us to the gym and showed us a few things that we can use throughout the season.
"If that's our time off then I'm not sure I'm looking forward to what Jim is going to do, but hopefully we will all feel the benefit of their work when the new campaign gets underway."