The Lancaster-based Pedal Heaven rider was edged out by defending champion Richard Bussell who completed the course around Rake, Hampshire, in 20 minutes and 35 seconds.
It is the third time Gullen has had to settle for second spot in a national championship.
Ryan Perry, who has already landed the titles over 25, 50 and 100 miles this year, came home third as riders tackled the hilly course in tough, windy conditions.
Pedal Heaven did however take the team honours with Gullen’s team mates Lloyd Chapman, fifth, and Joe Fry, sixth, also finishing well up the standings.
Gullen did win one race this week, finishing first in the final Tuesday night Salt Ayre Criterium of the season.
Bolton-le-Sands’ Jack Pullar, also of Pedal Heaven, took second spot.