But Murray is adamant that he still can turn his stuttering form around at the All England Club, where his bid to win a fourth grand slam title begins in less than a fortnight's time.
Thompson, ranked 90th in the world, was only entered into the main draw at Queen's four hours earlier after Aljaz Bedene withdrew injured, but the Australian played the match of his life to win 7-6 (7-4) 6-2.
The defeat is Murray's ninth already in 2017 and sixth against a player rated outside the top 20. It is the Briton's second-worst result by ranking since March 2012.
More concerning for Murray is not only the continuation of his poor form but the fact that he has lost potentially a week's worth of competitive matches on grass, with Wimbledon fast approaching.
It is perhaps no coincidence that both of his Wimbledon triumphs in 2013 and 2016 came after he also won the title at Queen's.
"It's a big blow, for sure," Murray said. "Obviously this tournament has given me great preparation in the past and, when I have done well here, Wimbledon has tended to go pretty well too.
"It's not ideal, obviously, but guys have in the past also gone in to Wimbledon having not won lots of matches. Novak [Djokovic] a number of times hasn't played any warm-up tournaments and played very well there.
"There is no guarantees that I won't do well at Wimbledon but it certainly would have helped to have had more matches."
Thompson had lost to Frenchman Jeremy Chardy on Sunday in the second round of qualifying but was handed a lifeline after Bedene pulled out with a wrist injury, though Murray said the late change of opponent made no difference.
"I found out quite a number of hours in advance so I was able to see quite a bit of him online and have seen him play a few matches before," Murray said. "I don't think that had anything to do with it."
The 30-year-old was also quick to dismiss suggestions that he had felt any extra pressure after pledging to donate his winnings from the tournament to the victims of the Grenfell Tower disaster.
Murray's first-round exit will earn him around £12,000.
"I don't think it's fair to place blame anywhere like that," he insisted.
"Obviously it's been a tough few months, no question about that, but when I'm playing, I'm just trying to concentrate on my tennis and when I'm away from the court I'm just trying to spend a lot of time with my family and the people that mean a lot or are important to me."
Thompson will go through to face American Sam Querrey in round two.