In 1619, prior to his father's death, Thomas Burnet younger of Leys was one of a body of Commissioners named by King James VI of Scotland, at the instance of Bishop Patrick Forbes, to visit the universities of Aberdeen.
Immediately on the subscription of the Covenant in Edinburgh, the powerfully organized body, known as the Tables, made arrangements for enforcing its acceptance throughout the whole country and gathering funds to support military detachments.
He and other Commissioners paid a preliminary visit to Aberdeen in early July 1638 where they were told politely but firmly by the town's magistrates and other leading citizens that they had no legal authority to exact the subscriptions demanded.
The university promptly denounced the Covenant as unlawful, and three of the leading preachers, Henderson, Dickson, and Cant, made a temporary retreat to the safety of Sir Thomas's Muchalls Castle.
Sir Thomas Burnett was one of the tribunal established to sit on 2 April in Greyfriars Church there and on following days, to force 'malignants' to subscribe to the Covenant under pain of confiscation of their goods.
At the same time Sir Thomas petitioned the Scottish Parliament for an exemption from excise and other heavy taxation being raised for Covenanting armies being sent to England, and for aid against marauding Highlanders.
Following the Proclamation of Charles II as King in Scotland, the Scottish Parliament adopted the most uncompromisingly covenanting character and its records for 1649 contain a complaint from Sir Thomas Burnett of Leys to the effect that he was owed £67,000 for supporting their cause.
Sir Thomas Burnett had co-operated with Bishop Patrick Forbes in removing 'abuses' in King's College, Aberdeen, and amending its discipline, although there is no trace of his having had a hand in its "purgation" in 1640.