Thompson, from Whistler, B.C., had a time of one minute 10.50 seconds. She was followed by teammate Georgia Simmerling of North Vancouver, B.C., in 1:11.07.
"I still feel like I could have been better in a few spots, but it was overall really good," said Thompson. "I felt like I fixed my mistakes in my training runs, so that was good. There's a smaller field here than most World Cups, but the Europeans all bring their strongest racers so it'll be a good field."
The top 16 women advanced to Saturday's elimination heats, which will feature four skiers racing each other down a course of turns, jumps and bumps.
"I'm definitely looking forward to racing now that qualifying's over," said Thompson, who won her second career Crystal Globe as overall World Cup champion last season.
Like Thompson, Simmerling is looking forward to testing her skills against top-flight international competition.
"We're both super-pumped to get in the gates with other girls, where it counts," said Simmerling. "I think (a medal) can definitely happen and I'm going to keep skiing smart and clean and fast. Hopefully that's what's going to happen."
Switzerland's Fanny Smith finished third in qualifying while Sweden's Anna Holmlund and Sandra Naeslund rounded out the top five. Smith won the inaugural World Cup race at Nakiska two years ago before finishing second behind Thompson last year.
In the men's qualifiers, Calgary's Brady Leman finished fourth in 1:08.16.
"I just had a mistake at the bottom of the course," Leman said. "It's so tight, you can't have any mistakes, but the rest of the run was OK so I guess we'll see."
After training hard in the off-season, Leman is hoping to improve upon his third-place showing in Nakiska last year.
"It's a lot of work to get back here every year," he said. "The first one is always so intense. It's going to be important to get out quick, for sure."
Austria's Johannes Rohrweck had the fastest qualification run of the day in 1:07.91. Teammate Anton Grimus and French skier Jean Frederic Chapuis rounded out the top three.
Montreal's Chris Del Bosco finished ninth in a time of 1:08.46 to also advance to Saturday's races.
"I was looking forward to a good start here - have a decent qualifier and then it's a whole different ball game," Del Bosco said. "I'm fired up for the season. I worked really hard this summer. Now it's time for the fun. We put in all that work, so we can have fun all year. Hopefully that will translate into some good results."
Four other Canadian men also made the 32-skier cut.
David Duncan of London, Ont., was 17th in 1:08.80, Ian Deans of Kelowna, B.C., was 19th in 1:08.83, Tristan Tafel of Canmore, Alta., was 22nd in 1:09.05, while Louis-Pierre Helie of Berthierville, Que., was 28th in 1:09.22.