Pan posted a time of 47.82 seconds in the morning session at the Aspire Dome pool, just over a second off the world record (46.80) he set on Sunday with his stunning lead-off swim in the relay won by China.
It was a rapid rebound for Pan following his surprising exit from the 200m freestyle heats on Monday, an event in which he was expected to contend for medals.
Italy's Alessandro Miressi qualified second in the 100m freestyle with 47.94, while Briton Matt Richards, the 200m freestyle world champion at Fukuoka last year, was fourth quickest.
With world champion Kyle Chalmers skipping the meet, along with Fukuoka minor medallists Jack Alexy and Maxime Grousset, Pan is in the box seat to pick up his first individual world title.
Swiss swimmer Desplanches, the Tokyo Olympics bronze medallist, secured top seed for the men's 200m individual medley semi-finals with a time of one minute 58.17 seconds.
Though France's 200m and 400m medley world champion Leon Marchand is skipping Doha, Fukuoka silver medallist Duncan Scott is present and eased into the 200m semi-finals with the eighth quickest swim.
Scott later helped Britain qualify quickest for the mixed medley relay final ahead of second-placed Australia and the third-ranked United States.
Denmark's Helena Bach topped the timesheets in a modest field for the women's 200m butterfly with a time of 2:09.21.
Tokyo Olympic silver medallist Siobhan Haughey will bid for a maiden world title in the women's 200m freestyle final in the evening session later on Wednesday, while Japan's Tomoru Honda, also a Tokyo runnerup, will swim for the men's 200m butterfly crown.
