The 23-year-old - a target for Tottenham Hotspur in this transfer window - missed the Toffees trip to Tanzania earlier this month because of the same issue.
Barkley is about to enter the final year of his contract and has told Everton he wants to leave the club this summer. Ronald Koeman said at the end of last season that he will be sold if he does not sign a new deal.
Defender Ramiro Funes Mori has also stayed at home from Everton's trip to boss Koeman's home country while he recovers from a knee injury sustained last season.
New signings Jordan Pickford, Cuco Martina, Michael Keane, Wayne Rooney and Sandro Ramirez are all in the squad.
The squad departed Liverpool Airport on Monday afternoon for Enschede in the east of the country ahead of a pre-season friendly against FC Twente on Wednesday. Everton will then travel to Belgium to take on KRC Genk on Saturday.
Full squad: Maarten Stekelenburg, Joel Robles, Jordan Pickford, Leighton Baines, Ashley Williams, Phil Jagielka, Callum Connolly, Mason Holgate, Jonjoe Kenny, Cuco Martina, Michael Keane, Morgan Schneiderlin, Davy Klaassen, James McCarthy, Idrissa Gana Gueye, Gareth Barry, Mo Besic, Tom Davies, Kieran Dowell, Kevin Mirallas, Aaron Lennon, Dominic Calvert-Lewin, Ademola Lookman, Wayne Rooney, Sandro Ramirez