The Reds will be without Peter Handyside and Lee Crooks despite both recovering from ankle injuries.
Gudjon told the official Barnsley FC website: "We had a setback today because I expected Peter Handyside to be fit for the Scunthorpe game. He is sick and cannot train.
"He has worked ever so hard during the week to be ready but is down with the flu and I cannot see him being fit enough to make the squad. That is a big blow for us.
"Lee Crooks is still a little away because he picked up a deadleg in training that will keep him out for another five or six days. He will not be able to train until after the weekend".
Barnsley will be without Paul Warhurst again due to him being cup-tied.
However, Brian O'Callaghan has suffered no reaction since his return from a groin injury and will start.
Peter Beagrie (hamstring), Nathan Stanton (shin) and former Reds loan player Mark Jackson (ankle) are all doubtful for Scunthorpe.