The 18-year-old felt he was just starting to establish himself in the first team at Hearts when he picked up a knee injury in a collision with Aiden McGeady at Parkhead in December.
The subsequent spell on the sidelines proved more difficult than Thomson imagined and he says the club's physio, Rob Marshall, often bore the brunt of his frustration.
"It was unbelievable how bored I was during the time I was out injured – it was a nightmare," said Thomson, who had enjoyed a stunning start to the season after being handed his competitive debut against Dinamo Zagreb in the Europa League.
"I was starting to do well in the team when I sustained the injury – I picked it up when I tackled Aiden McGeady and he ran into my knee – and I was gutted about that.
"The team then started to do well when I was out and I was beginning to wonder if that was because I wasn't there. You begin to have thoughts like that when you've got too much time on your hands.
"I just had to keep working hard and the physio has helped me a lot over the last couple of months. I thought I'd be back a lot sooner than I was but it's just as well I wasn't as I am feeling really good now.
"The physio and me fell out a couple of times as I felt I was okay to start training but he insisted I wasn't.
"He said on a couple of occasions that it was up to me but I'm glad I listened to him and kept doing my rehab as it has been the right thing."
Thomson, who made his SPL debut in a 2-2 draw against St Johnstone in Perth and was voted the Clydesdale Bank Young Player of the Month for September, has been broken in gently again by Jim Jefferies, the teenager having come on as a substitute in the last two games against Hibs and Rangers.
He's hoping to be involved again at some point in tomorrow's trip to face St Mirren as Hearts bid for a win that would signal a massive step in their bid to secure a place in the top six after the forthcoming split.
"I've come on in the last two games and, though that was probably down to injuries, I'm glad to get back playing," added Thomson.
"My touch hasn't been the best since I came back but that's just down to not playing games after being out for three months. Hopefully, I can get that back as soon as possible and start playing as many games as I can between now and the end of the season.
"It was a good result against Hibs and I think we could have won by a couple of more goals that day if we'd taken our chances. I thought we were better team.
"Against Rangers, I thought we were a bit unlucky to lose 4-1 as the goals they scored weren't really down to good football – they were more down to our mistakes.
"If we can cut those out of our game, I am confident we can have a good end to the season and, hopefully, a good start to next season as well as Jim has been brilliant since he came in.
"If we win our next two games, we'll be in the top six, although it was a bit of a blow to see St Johnstone give themselves a huge boost in their bid to overtake us by beating Rangers the other night.
"If we get into the top six, we can hopefully kick on and climb a place or two in the closing weeks of the season."
One of the games Thomson missed during his lay-off was the defeat by St Mirren in the semi-finals of the Co-operative Insurance Cup at Fir Park – a game that fell less than a week after Jefferies had taken over from Csaba Laszlo.
According to Thomson, the mood in the Hearts camp has brightened considerably since then – and much of the credit for that, he says, has to go to first-team coach Gary Locke.
"I was gutted having to sit in the stand and watch that semi-final," he reflected.
"Everyone wants to play in games like that and, while not trying to blame the pitch, it was a terrible surface that night.
"It was a disappointing result for the club but one of the good things since then is that Jim, Billy and Lockey have shown that they are not scared to take a chance with young players. If you are doing well in training and showing you are capable of doing the business for the first team, then you are going to get the chance to flourish.
"Gary Glen is getting a run of games, for example, and he's certainly not let anyone down. Jamie MacDonald also got his chance last weekend due to injuries and he'll now be looking to hold on to that position.
"It gives the young players, even those younger than me, a buzz because they know, if they do well, they've got a chance of making the first-team squad.
"Csaba helped me out a lot as well but the support I've been given by Jim, Billy and Lockey since they came in has been fantastic. The buzz Lockey has created is amazing. We never had that before. That's what has helped make the place a lot happier. His enthusiasm for the role is there for everyone to see. He's so happy to be here, always has good banter and I think that's what we needed about the place."
Thomson, who has two more years on his current deal after the end of this season, is currently in the Scotland Under-19 squad, though his breakthrough into the Hearts first team stopped him from being involved at international level earlier in the campaign.
"I've only been able to go to one of the four games – a friendly in Germany that we drew 0-0," he said. "Csaba didn't want me to go away with the Under-19s because it was more important at that time for me to be playing first-team football for Hearts and you can understand that.
"However, I would love to keep trying to get higher and higher with Scotland and the Under-21s are next on the ladder but it depends on whether I get picked or not. I've just got to try and keep playing well for Hearts."