In July it was the clash between Victory's sold-out exhibition match against Liverpool and the Socceroos' participation at the East Asian Cup in South Korea.
National team commitments won out on that occasion, forcing Thompson to watch his club colleagues go up against Luis Suarez and Steven Gerrard on a laptop in his Seoul hotel room.
And October is set to bring another test of his loyalties, with Australia's glamour friendly against France on October 11 scheduled for the same week as the A-League opening derby against Melbourne Heart.
Today the 34-year-old striker said he wasn't looking forward to being caught in the middle of another potential club-versus-country tussle.
"I got put on the spot a couple of weeks ago," Thompson said. "Would you rather be in Korea or would you rather be playing Liverpool?
"I tell you, it wasn't fun over there chasing the Koreans and the Japanese, and it looked fantastic (at the MCG).
"It's a tough one. I'd obviously love to play, I'd love to be selected or be in contention (to play France). We'll see what happens. Obviously I'd (also) love to play against Heart."
Thompson agreed with suggestions national team coach Holger Osieck could choose to omit Australian-based players for the match against Les Blues in Paris, but would not welcome being left out of the enticing fixture.
"I think that could be an option for him," he said.
"I want to be part of every Socceroo game because it's a World Cup year. You've always got to put your hand up to be available, whether it be the first game of the season – the big Melbourne Heart game.
"You're going to miss big games sometimes. Like I said, it's a World Cup (year), you want to be part of everything."
At a loss as to why Football Federation Australia chose to schedule the start of the domestic season in the same week as FIFA-sanctioned international fixtures, Thompson wants to avoid a repeat of such a clash in the future.
"If I knew, I'd probably be doing their job," he said. "It's a tough one. You're dammed if you do and you're dammed if you don't.
"Pretty much all countries' leagues stop I'm pretty sure, so I can't see why ours shouldn't."