Charles will visit Glendelvine Estate, near Dunkeld in Perthshire, to learn how the recovery of the species is being helped by the trapping of invasive grey squirrels in the area.
The red squirrel, a native species to the UK, has increasingly come under threat from the non-native grey species.
The estate's keeper David Fraser has been successfully working with the Scottish Wildlife Trust on their project Saving Scotland's Red Squirrels since 2009.
In 2011, 63 grey squirrels were trapped, with that number almost halving the following year and the species is now seldom seen on the estate.
The visit is part of a week of Scottish engagements for the Duke and Duchess of Rothesay.
The Duke will later attend a reception for the Scottish Wildlife Trust's 50th anniversary at Murthly Castle, near Perth.
He will also pay a visit to Balhousie Castle in Perth and tour the Black Watch Regimental Museum, which reopened last year after a £3.5 million redevelopment.
Charles is Royal Colonel of the Black Watch, 3rd Battalion The Royal Regiment of Scotland, as well as patron of the Black Watch Royal Highland Regiment Association and of the Black Watch Heritage Appeal.
Meanwhile the Duchess will be in Edinburgh to pay a visit to the Shortbread House bakery in the city's Tennant Street.