Athens-based Atromitos finished fourth in the Greek Super League last season, 23 points adrift of champions Olympiacos, who drew 1-1 with Newcastle in Portugal last month.
Pardew told the club's official website, nufc.co.uk: "It will be a hard game, for sure. You don't finish fourth in your league unless you've got something going on, so they are obviously on the up.
"It's a tough journey which is going to take a little bit away from us.
"Certainly coming back from there to go to Chelsea on a Saturday is not ideal."