The Wars of the Covenant covered the years between 1638 and 1651, when Scotland and England were two independent countries, though both were subject to King Charles I. The cause of the Covenanter movement lay in the attempts of the Stuart Kings to impose Anglicanism on a basically Presbyterian Church of Scotland and to make the Stuart kings head of the Church of Scotland in line with their position in the Church of England.

In 1638 a National Covenant was subscribed to throughout Scotland, which demanded that general assemblies and parliaments be free of royal control. Charles duly raised an army in England to subdue the Scots. After many military skirmishes and battles both in Scotland and in northern England, in 1647 King Charles I surrendered to the Scottish Army, which handed the king over to Oliver Cromwell. King Charles I was executed in London. England became a republic while Scotland chose to remain a kingdom. Charles's son returning from exile in the Netherlands, was crowned at Scone as King: Charles II of Scotland. In response, Cromwell's army invaded Scotland and defeated the Scottish Army of the Covenant in 1650. Thousands of Scots were taken prisoner, and may were transported for sale to the plantations or colonies in America and the West Indies. King Charles II escaped to exile in Holland, where he remained until the Restoration of 1660.

In 1685 King Charles II was succeeded by his brother as King James VII of Scotland and King James II of England and Ireland. King James, however, was a Catholic--something unacceptable to the Protestants of England and of Scotland. In 1689 the Scots Parliament offered the crown to William of Orange and his wife Mary Stuart. This was opposed by followers of King James II, and his Jacobite Army clashed with a government army in 1689. This, and the Battle of the Boyne in Ireland in 1690, ended the rule of the Stuart kings.