The Ibrox left back started both tournament warm-up matches against Armenia and Belgium but has been replaced by 19-year-old Josko Gvardiol of Dinamo Zagreb for the Wembley clash.
Barisic made 52 appearances for Rangers last season and was expected to be Croatia’s first choice left back for the tournament.
However, the 20-times capped defender has not even made the bench after the squad was cut from 26 to the 23 permitted for matches.
An injury may be behind his absence after head coach Zlatko Dalić revealed the 28-year-old has been struggling.
He said: "I think this is the best possible option for this match.
"Gvardiol has come in at left-back as Barišić has had some problems in the last ten days."
Croatia and England are in the same group as Scotland, who start their Euro 2020 campaign against the Czech Republic at Hampden on Monday.