The 22-year-old, who was diagnosed with leukaemia aged seven before going into remission five years later, carded an eight-under 63 at Silkeborg Golf Club.
A group of six, including England’s Matthew Baldwin, are two shots back with a total of 18 players inside the top 10 as scoring is good.
“It’s fantastic to get off to a great start for a change,” said the 6ft 9ins Thomson, affectionately known as ‘Jigger’, who is battling to secure his playing privileges for next season.
“I have been playing some great golf recently but not scoring, so to get off to a low-scoring start today was great.
“I had a good lesson on iron play in Prague last week and it has really tightened up my iron play and given me more opportunities to give myself more birdie chances.
“Last week I played fantastic and didn’t hole anything, whereas today I played to a similar level and holed some putts.
“It would be great for me to have a positive result this week. I had a terrible start to the season and really positive result would give me a huge confidence boost going into the rest of the season.”
In the race for the final automatic qualifying place for the Ryder Cup team English duo Matthew Fitzpatrick and Eddie Pepperell opened with rounds of 72 and 70 respectively,
Both need to win to potentially dislodge local favourite Thorbjorn Olesen, who shot a 73.