Gary Leaburn, 25, and Derek Taylor, 19, were killed when a stone wall they were helping to repair collapsed on top of them.
The Crown Office said the decision to prosecute was taken "after careful consideration" by the office and the procurator fiscal at Inverness.
The charges are being brought under the Health and Safety at Work Act 1974.
Mr Leaburn and Mr Taylor were among 13 Prince's Trust volunteers from Dundee working to repair a wall at Garso Wick, on North Ronaldsay - northernmost of the Orkneys.
Elizabeth Crowther, executive director of The Prince's Trust Volunteers, said: "All of us at The Prince's Trust Volunteers are deeply distressed by this tragic accident.
"Our sympathies are with the families of the young men who died and with the other team members who were present at the time. We have worked closely with the authorities investigating the tragedy and will continue to do so. It is so important that everything possible is done to ensure that nothing like this happens again."