The former Scotland midfielder was sidelined for the final two Premiership fixtures due to a thigh injury picked up in the 1-1 draw with Partick Thistle at Easter Road.
It left Thomson watching from the stands as defeats against Ross County and Kilmarnock condemned Hibs to a relegation play-off.
They will face either Hamilton or Falkirk in their play-off, the first leg of which is on Wednesday, and Thomson expects to be fit enough to take part. The 29-year-old said: "It was massively disappointing not to be available for the Kilmarnock match - watching from the stands was a really frustrating experience.
"But I'm confident I will be fit enough to be available for selection for the play-off and that's all I'm working towards at the moment.
"There are two games left in order for us to keep the club in the Premiership and we will all be giving everything we can to make that happen. We need to show we've got the quality, attitude and desire to come out on top."