Pan clocked 46.80 seconds, eclipsing the previous mark of 46.86 set by David Popovici of Romania, as the opening day of the event finished with a bang.
The amazing swim lifts the teenager into favourite for the 100m gold medal at the Paris Olympics.
Pan flirted with record pace at the Asian Games in Hangzhou last year.
He became the first Asian swimmer to break the 47 seconds barrier in the event and clocked an incredible 46.65 in a relay leg. A record can only be set in a lead-off leg in a relay.