The west Londoners secured safe passage to the third qualifying round with a dominant 4-0 victory over Northern Irish part-timers Crusaders, making it 7-1 on aggregate over the two legs.
The match was Fulham's fourth competitive match of the season, having started their European campaign against Faroese minnows NSI Runavik on June 30.
Off and running: Fulham celebrate opening the scoring against Crusaders at Craven Cottage
But despite the early start, Hughes has quashed concerns that it could adversely affect their preparations for the Barclays Premier League.
'It hasn't been too difficult to adapt to the early start,' he said. 'We've tried not upset our pre-season, if you like.
'The games are slightly different because they are competitive but we're still working through things in training with the new season in mind.
'Obviously we maybe have to tweak one or two things in the build-up to competitive games, but I think once we knew we were coming back early it was definite then.
'You get your head round it and you carry on'
Early start: Fulham's Andrew Johnson helped his side progress in the Europa League
Andrew Johnson, Damien Duff, Bobby Zamora and Steve Sidwell netted in the second leg at Craven Cottage to set up a tie with RNK Split of Croatia.
Hughes admits that he knows little about next week's opponents but promises that the Whites will not take their trip to the Adriatic coast lightly.
'We go where we have to go,' he said. 'We take each game as it comes, wherever that may be.
'We're still in the competition and we'll enjoy it as much as we can for as long as we're still in it.
'We will do exactly the same as we would do if we were going to play Manchester United.
New boy: John Arne Riise made his Fulham debut against Crusaders
'We will have a couple of guys maybe go out and watch a couple of their games and bring reports back.
'Leading up to the game, we will watch a couple of DVDs, have a little chat about certain things.
'Maybe certain things that we feel they're dangerous at and certain areas where we feel we can hurt them.
'It will be no different to preparations for a Premier League game really so we will know enough about them come kick off.'
CzechRepublic Under-21 international Marcel Gecov could make his Fulham debut in Croatia next week after completing his move from Slovan Liberecthis week.
Fellow new boy John Arne Riise made his first appearance for Fulham last night and Hughes believes the former Liverpool man is settling in well already.
'He is a very, very good acquisition,' he said. 'It is almost as if he has been here for two years.
'It hasn't been a massive thing in the changing room, he just kind of slipped in quietly straight away.
'He has obviously got his brother (Bjorn Helge) and Brede [Hangeland] here already and he knows Danny from Liverpool.
'He has integrated straight away but you find that with any of the new players that come to this club.
'We've got a good bunch of lads here and people seem to fit in straight away.'
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