The 41-times-capped forward needs surgery on a shoulder injury sustained earlier this season and will go under the knife later this week.
The 26-year-old will swap Glasgow Warriors for Welsh RaboDirect Pro12 rivals Scarlets this summer but his operation means he will miss Scotland's trip to South Africa for a tournament involving the host nation, Samoa and Italy.
Interim head coach Scott Johnson - who it was confirmed yesterday would continue in his role for another 12 months before making way for New Zealander Vern Cotter - has no plans to replace Barclay in his 30-man squad.
Meanwhile, the SRU has also confirmed that Scotland's opening Autumn Test against Japan will be played at Murrayfield.
The match, on Saturday, November 9, with a 2.30pm kick-off, will be the fourth occasion the countries have met in a cap international.
Scotland have also played Japan five other times when caps were not awarded, most recently in 2010, as a precursor to the summer tour to Argentina when a Scotland XV won 24-5 in Edinburgh.
The November game against Japan is the first in a series which will see Scotland face South Africa on Sunday, November 17 (3pm), and Australia on Saturday, November 23 (6pm), also at Murrayfield.
Scottish Rugby's Director of Commercial Operations, Communications and Public Affairs, Dominic McKay, said: "The demand from Scotland supporters to watch the national team has grown this season and, with that in mind, we are keen to enable as many people as possible to be able to watch Scotland next season.
"With five internationals at Murrayfield next season - including our 2014 RBS 6 Nations Championship games against England and France - we'll be announcing details shortly of a Scotland season pass, at a range of prices, which is our way of thanking our loyal supporters.
"We are also committed, when appropriate, to continue to make the Scotland team accessible to people throughout the country.
"This week, as part of the squad's preparations for this year's summer tour, the players and coaches are in Perthshire and Morayshire and will open the door to the public to come and watch them practice."
Tuesday afternoon's squad training session at Grantown Grammar School in Grantown-on-Spey is open to the public from 2pm to 4pm.