Bailey, 16, died following the incident at Cults Academy on 28 October.
A 16-year-old boy - who cannot be named for legal reasons - has been charged with murder.
A newspaper noticed stated: "Following the sad loss of Bailey, a private funeral will be held. Bailey's family would like to thank the community for their kindness and support."
The accused, who was remanded after appearing in private at Aberdeen Sheriff Court, is also charged with having a blade or point on school premises.
A private funeral is to be held for Bailey Gwynne, who died after being stabbed at his Aberdeen school.