Charles was the eldest surviving son of Charles (I) and Henrietta Maria. He was twelve when the Civil War broke out. Until then he had been raised in the stately magnificence of Charles's royal palaces and had received a good if not extensive education. He rapidly became skilled in the arts of war, fighting alongside his father in the early engagements and being made commander of his troops in the West Country in March 1645, when only fourteen. As the tide of the war changed, however, Charles wisely left England, settling first (1646) in France and then (1648) Holland, where his sister, Maria, the Princess Royal, had married Prince William of Orange. Charles had at least two sexual encounters during these years, and probably more. Rumours persist that he had fathered a son, James, while in Jersey in 1646 but of more significance was a second son, also called James, born in the Hague on 9 April 1649. The mother was Lucy Walter. The son, who became the duke of Monmouth, later claimed his parents were married and that he was the legitimate heir to the throne.

It was while living in the Hague that Charles learned of his father's execution. On 16 February he was proclaimed king in Jersey. A few days later the Scottish Parliament proclaimed Charles their king, provided he was prepared to accept the Scottish Covenant. This widened the rift between Scotland and England, where the new Parliament abolished the monarchy in March 1649. Charles really wanted to be king of England, and accepting the Scottish Covenant would have barred that route completely. Charles learned early on, therefore, that he needed to be cautious and devious. He was a remarkably pragmatic individual whose main aim was to enjoy himself, but he was prepared to fight and prove himself. He felt that everyone should be allowed to lead their own life, and thus he would bend with the wind and take whatever options best served his purpose. He therefore bided his time, exploring what other avenues might exist. He found Ireland closed to him by Cromwell's army while, in April 1650, an unofficial advance guard under the command of James Graham, the marquess of Montrose was defeated and Montrose hanged. Charles had to act so, in June 1650, he signed a treaty which he managed to keep sufficiently ambiguous but which effectively made him a covenanted king of the Scots. Twelve days later he landed in Scotland, a stranger in his own land. He was dubiously accepted as king but not allowed to exert any authority. He was more a figurehead than a sovereign, but his very presence posed immense danger, not only from rival factions in Scotland but from the English. A month later Cromwell led an army into Scotland. It was not overtly an invasion force, rather a move to explore the relationships between the two countries, but it left little doubt that Cromwell meant business if he met any opposition. However, as many past campaigners had found, Scotland is a difficult land to conquer without a massive support infrastructure and Cromwell's was disrupted by weather and disease. Nevertheless he engaged and overwhelmingly defeated a Scottish force at Dunbar on 2 September 1650, taking possession of Edinburgh and Leith. This was the downfall of the government of Covenanters under Archibald Campbell, marquess of Argyll, and the chaos that followed saw an untrusting but necessary alliance between the extremist factions who overthrew the anti-Royalists (known as the Remonstrants) and proclaimed Charles their king. He was crowned at Scone on I January 1651.

Cromwell continued to stamp his authority on Scotland, and in July 1651 Charles led a hopeful army south into England. He was met by Cromwell's army at Worcester on 3 September 1651 and soundly defeated. Charles was lucky to escape with his life. He fled into Shropshire and sought refuge at Boscobel House, where he was helped by the yeoman Richard Penderel. It was at this time that the famous episode happened of Charles hiding in an oak tree whilst Cromwell's soldiers scoured the woods. Charles disguised himself as a servant and a few weeks later made his escape to France. It was difficult for Charles to disguise himself as he had a most distinctive physique. He was tall, at last six feet three inches, which is surprising considering the shortness of his parents. He probably inherited the genes through his Danish grandmother.

He spent the next eight years on the continent, wheeling-and-dealing with whatever power might assist him. He was well placed, as during the next few years England found itself at war with first the Dutch (1652-54) and then Spain (1656-9). Charles took advantage of both conflicts to gain support for his own cause. These hostilities brought the English closer to the French as allies, which further helped Charles because of his own close affinity with the French. An Anglo French force defeated the Spanish in northern France in 1658, as a consequence of which the Spanish surrendered Dunkirk to the English, who once again held territory in France.

During this period Cromwell's hold on England and Scotland grew. The Commonwealth was declared and, in 1653 Cromwell was made "Lord Protector". Though he governed through a Parliament, he was granted almost absolute powers and, indeed, in May 1657 Cromwell was offered the title of king. He refused but accepted the right of succession, so that his son, Richard, would be Lord Protector after him. For a brief period religious tolerance was observed throughout England and the Jews were readmitted, but towards the end of Cromwell's government there was a backlash against puritanism and extremism, and a return to a more Catholic practice. Nevertheless civic marriages were allowed and the registration of birth, deaths and marriages enforced.