Now that he is at Raith Rovers, the 27-year-old is wary of history repeating itself. He will lead the Fife side out against the Tynecastle side today hoping to keep up an impressive start to the SPFL Championship season.
He will likely look out for Neilson blocking his path, albeit if it is only to offer a friendly handshake. Thomson was emerging form the Hearts youth system as a promising right-back when Neilson was still a player, with the senior man proving to be so consistent in defence that his young protege barely got a look in. Indeed Thomson's breakthrough season quickly broke down.
He does not resent Neilson, though. Rather the Raith captain is full of admiration for the 34-year-old who became a Scotland internationalist at Tynecastle and is now head coach at the Edinburgh club. His progress has not taken Thomson by surprise.
"I didn't play much with Robbie because if he was playing, I wasn't," he recalled. "He kept me out of the team quite a lot because, just when I was breaking through, he was a really consistent player.
"That would have been when he won his Scotland cap. I was at Hearts for nine years, I was still there when he left to go to Leicester. But Robbie was a good guy in the dressing room and you could tell he was going to go on and do coaching, move into management. He was good with me."
That positive influence was never more keenly felt than during the more tempestuous parts of Vladimir Romanov's nine years at the helm at Tynecastle. "You could go and talk to Robbie about a problem . . . he was one of the few English speakers in that dressing room, so he didn't have much of a choice!" added Thomson with a smile.
There is a degree of truth behind the humour. Thomson was at Hearts when the club reputedly had 60 senior players on the books, many of whom were obscure names from Lithuania or further afield. Some would never a kick a ball for the club. During one transfer window 11 new faces arrived on deadline day.
Thomson cites Neilson as his point of reference and stability during a wild ride in Gorgie. "At times, Robbie had to be a rock of stability in that dressing room. This is going back a few years now, but he always said his piece when issues arose. And during my time there, we had more than one issue," he said.
"You need guys like that in a team, players who can stand up and be counted. And he was always the right sort of big character to make a manager. You could tell."
Adam Eckersley knows the type. The 28-year-old signed for Hearts this week on a contract until the end of the season but his career path started at Old Trafford. As a youth prospect at Manchester United, he came into contact with many big characters - he trained alongside the likes of David Beckham and Roy Keane - and is convinced that has given him the grounding he will need to make a good impression with Hearts.
"I could not ask for a better upbringing," he said. "I remember playing against Beckham in training when I was young and I was meant to be marking him but he was swinging balls in and Ruud van Nistelrooy was putting his head on the end of them.
"Keano was on my team and he turned round to me and said, 'will you stop those f****** crosses'! I just looked at him and I was thinking in my head: 'the best full backs in the world can't stop these crosses and I'm 18. What is it that you want me to do?' I s*** myself and just said, 'okay Roy'. I got in my car as fast as I could after that, drove home and tried to forget about it."