First, and not least, there was stepping into the shoes of his old man, Eddie, a figure adored by the Tannadice faithful, and then along came Charles Green.
In recent weeks, after a bit of a contretemps, Thompson has returned to the board of the Scottish Premier League, having stepped down just three months ago. He appears to have his father's combative instincts and nose for a challenge, despite being different in other ways.
The 46-year-old has lain low since the tiff with Rangers came to a head last month but, for United, that all ended satisfactorily. Green, the Rangers chief executive, and the Ibrox side went to Tannadice in the William Hill Scottish Cup and lost 3-0, with their officials and those of United not even passing the time of day together.
"It's done, it's gone now," says Thompson. "Prior to that match we had to put up with an awful lot as a club, but we chose deliberately not to talk about it or crank it up; plenty others were doing that.
"When Rangers came here we did what we had to do – we beat them on the pitch. We also had a great turnout that day from our fans in the face of the boycott; in fact the crowd was about the normal size. And we paid Rangers their due – I think it was about £30,000 or so from memory – pretty soon after the tie."
And Mr Green? Has there been any kissing and making up since? "I never saw Charles Green or any Rangers directors that day at Tannadice; they didn't come into the boardroom," says Thompson.
"Fine. It was their choice. I'm not going to talk about Charles Green, except to say this: I think he has done a good job so far for Rangers. It is time we all moved on."
In the midst of all this Thompson had to find a new manager, after Peter Houston announced he was leaving at the end of the season and the Tannadice directors decided to hurry him along. By January 28, Houston was out. And by January 30, Jackie McNamara was in.
So far Thompson's choice looks richly vindicated. In his opening game, the new manager put Rangers to the sword and, notwithstanding a dire 6-2 defeat by Celtic last week, has now won three out of four with United.
Despite his fine record at Partick Thistle, some doubted that the softly-spoken McNamara was ready for the step up. But not Thompson.
"Jackie was incredibly impressive in our interview with him and has been like a breath of fresh air at this club," he says. "I'm not going to knock Peter Houston: he was here for six years in total, and as manager was highly successful. But Jackie is a different guy and is very, very impressive.
"Appointing him was a risk, of course it was. But bringing in any manager is a risk. History will remember Jackie as being my first real appointment as chairman. With Peter [Houston] we just sort of fell into a working relationship when Craig Levein left. So Jackie is basically my first big call here. He has won three out of four so far and I think our fans like what they are seeing."
Time will tell how wise the appointment was; so far it looks very good. But what isn't in doubt is that McNamara was a cheaper option than retaining Houston. United, like most Clydesdale Bank Premier League clubs, are slashing costs and an inexpensive manager from a lower league was just about a necessity following Levein and Houston.
Eddie Thompson, originally a west of Scotland businessman, came to love United and lavished money on the club. It is an albatross that will hang forever around the neck of his son.
"My father put ridiculous sums of money into this club – all told maybe about £5.5m worth if you factor in share-purchases and other things," says Thompson. "Only recently my family has also injected another six-figure sum, which will stand there as a loan.
"It's a fight for every SPL club. If you look at our most recent accounts to June 2012, we made a decent profit, but only after selling David Goodwillie [to Blackburn Rovers for £2m plus add-ons]. Our debt is down by about a third, to roughly £3.7m compared to over £6m a few years back.
"It is a question of football ambition versus financial responsibility. You can't toy with your banking facilities. I'm not digging up the banks but these days they expect some form of debt-reduction. So we have had to reduce our costs while also aiming for success on the park.
"Dundee United actually has lower bank debt but higher loans today compared to the period before David Goodwillie was sold. So I think that tells you about the commitment my family still has to this club."
Four years on after Eddie's death, does he ever tire of the patriarchal shadow hanging over him? "I'm different from my dad, everyone knows that. I think it took the fans quite a time to get to know me and accept me.
"It has been a challenge stepping into his shoes here; it is the whole 'father's footsteps' thing. We were close but I'm my own man and I think I'm doing okay - aye, I'm doing fine."
The mysterious business of Thompson stepping off the SPL board and then re-joining it again two weeks ago is scarcely worth going into - a tiff has been resolved behind closed doors.
But what his re-emergence does mean is that Thompson, along with fellow board members Neil Doncaster, Eric Riley, Duncan Fraser and Michael Johnston, will be an influential voice in the whole 12-12-18 league reconstruction palaver over the next few weeks.
Thompson is all for the new model, having originally worked on the early draft of it months ago. "It is not a perfect solution, but I think it's the best we've got. I think we need to get this structure over the line and go with it, otherwise we'll be stuck with what we've got for years. I've met our fans, ArabTrust, our business supporters and I've laid out to them what we feel as a club.
"There are no other options on the table. There are a lot of positives around it and I think the TV people are making positive noises about the 'middle eight' after the proposed split [after 22 games]. I think 12-12-18 is by no means perfect but is for the best. The fact is, there is no perfect solution."
Our conversation over, Thompson then began enthusing in small-talk about Dundee United's youth policy, and the gems he can see coming through. Was it not ever thus at Tannadice?