Its registers include a wide range of material on the political, administrative, economic and social affairs of the Kingdom of Scotland.

The council supervised the administration of the law, regulated trade and shipping, took emergency measures against the plague, granted licences to travel, administered oaths of allegiance, banished beggars and gypsies, dealt with witches, recusants, Covenanters and Jacobites and tackled the problem of lawlessness in the Highlands and the Borders.

After the restoration of the monarchy in 1660, Charles II nominated his own privy councillors and set up a council in London through which he directed affairs in Edinburgh, a situation that continued after the Glorious Revolution of 1688–9.

The Register of the Privy Council of Scotland (1545–1689) was edited and published between 1877 and 1970 by John Hill Burton, David Masson, Peter Hume Brown and Henry Macleod Paton.

Article 19 of the 1707 treaty stated that "after the union the queen’s majesty and her royal successors may continue a privy council in Scotland, for preserving of public peace and order, until the parliament of Great Britain shall think fit to alter it, or establish any other effectual method for that end".

[1] The abolition of the Privy Council of Scotland occurred on 1 May 1708, twelve months following the Treaty of Union coming into force.

Due to there being no formal government departments in the Kingdom of Scotland during the councils operation, it was the only forum to exist which allowed policy matters and decision making to be discussed.

The Lord President of the council was accorded precedence as one of the King's chief officers in 1661, but appeared in the Estates of Parliament only intermittently.