He has now returned to full training and first team coach Mark Proctor says he is making good progress.
He told BBC Tees: "Let's hope we can get him back on the park with a couple of games under his belt before the end of this season."
The Scotland international joined Middlesbrough from Rangers for ?2m in July 2010.
He managed just two league games before fracturing his fibula.
He briefly returned to action towards the middle of the season but a further fracture was eventually found, keeping him sidelined for most of the campaign.
But Thomson is expected to play first team football again before the season is out.
Proctor added: "He's had a couple of games and has managed to complete a couple of 90 minutes.
"Psychologically I think it will be good for him to get back out there."
But he conceded that it will be some time before supporters get to see the best of the former Hibernian man.
He said: "I think he's looking forward to next season and showing Middlesbrough fans what he's all about."
Source: BBC Sport
Source: BBC Sport