Olympic champion Van den Hoogenband, well beaten by Thorpe in the 200 freestyle final, posted the fastest time in Wednesday's semi-finals, 48.39 seconds.
But Popov, winner of swimming's blue riband event at two Olympics and two world championships, was only a whisker behind in 48.51, having led the Dutchman with the fastest 50-metre split of 22.91.
Thorpe, by contrast, trailed sixth in his semi-final at the 50-metre mark but accelerated down the return length to finish in a personal best 48.71.
Popov, who moved to Switzerland this year after a decade in Australia, lost his Olympic title to Van den Hoogenband at the 2000 Sydney Games.
The Russian missed the 2001 world championships because of illness but, at 31, is far from a spent force, as he made abundantly clear in the 4x100 freestyle relay in which he finally anchored Russia to victory.
"I wasn't looking at Popov, only at the yellow wall. But it's going to be very, very tough tomorrow because Popov is in good shape," Van den Hoogenband said.
THORPE SEQUENCE
Van den Hoogenband was beaten to the 100 freestyle gold at the 2001 worlds by American Anthony Ervin, while Thorpe was fourth in that final.
Thorpe seeks his fourth gold medal of the championships, having taken his overall tally of titles to 11 when anchoring Australia to victory in the 4x200 freestyle relay on Wednesday.
He will also make his first foray on the world stage in the 200 individual medley, an event in which American rival Michael Phelps is also competing. Phelps, chasing four individual titles, retained his 200 butterfly crown on Wednesday.
Japan's Kosuke Kitajima, with one world record to his credit in Barcelona, will put a second mark under threat in the men's 200 breaststroke final.
Kitajima clocked 2:09.73, the second-fastest time ever, in Wednesday's semi-finals, two days after breaking the 100 breaststroke world record in winning Japan's first-ever world title.
KITAJIMA CONFIDENT
Kitajima lost the 200 world record to Dmitry Komornikov, who swam 2:09.52 in June, but Komornikov looks less of a threat this time, finishing well behind Kitajima in the semi-finals.
Spain will hope its adopted favourite, Russian-born Nina Zhivanevskaya, bring gold in the women's 50 backstroke However, the European champion must first dispose of the likes of Ilona Hlavackova of the Czech Republic, vastly experienced German Sandra Voelker and American defending champion Haley Cope.
Poland's Otylia Jedrzejczak, the world record holder and Barcelona 100 butterfly silver medallist, established herself as favourite to succeed absent Australian Petria Thomas as women's 200 butterfly world champion with the fastest semi-final time of 2:08.42.
American Mary Descenza and 17-year-old Hungarian Eva Risztov, the 400 freestyle silver medallist, are best placed to deny her.
