The Potters fly face Thun on Thursday in the first leg of a play-off which, if successful, would put them into the group stages of the Europa League.
And while Pulis has no worries about having to squeeze the two games into a busy start to the domestic campaign, he is concerned about the prospect of playing on a plastic pitch.
"What I am disappointed and annoyed with is the fact it is not on grass, the trip is going to be particularly tough because we will be playing on artificial turf," said the Stoke boss.
"It's a big disadvantage to us when we are up against a good side with an excellent home record who are top of their league.
"If you are going away and playing on grass that is fine but to fly to a country and have to play on an artificial pitch is a big call.
"You only have to look at their home record, it is outstanding, and they won 5-2 on Sunday and play very well on their surface.
"When I was a youngster I played at QPR and Oldham on their artificial pitches and I found it very difficult as a player.
"The bounce was completely different so it will be interesting but for me it gives them an advantage without a question of a doubt.
"We have one (an artificial pitch) here but it is a different type to the one they use so it will be about how we cope with playing on it.
"And you don't want to train too much on it because it is renowned for taking a lot out of players who are not used to working on it.
"It's difficult enough just learning about going away in Europe and trying to get results, but the conditions makes it doubly difficult."
FC Thun beat Lausanne Sports and have a two-point lead are top of the Swiss Super League after seven matches.
Stoke opened their Premier League campaign with a gritty goalless draw at home to Chelsea.
Pulis believes that will stand them in good stead as his side go looking for a fourth successive clean sheet in competitive matches, having also shut out Hajduk Split over two legs in the previous round.
"We will play the same way we went to Split. We will do the best we can - they are a good team who are very organised - very close in their set-up to German teams - and they play very well on that surface," said Pulis.
"They are not a name team but we know it will be a tough game because they knocked out Palermo, who are a good Italian side.
"It is not as though we have the experience so we are learning as we go forward and we have a good group of players who are desperate to play on Thursday.
"The biggest worry for us will be the artificial pitch and how the players respond."