Charles was born the third but became the eldest surviving son of Sir Thomas Vavasour of Copmanthorpe, County York, and his wife Mary Dodges.
During the Irish Rebellion of 1641 Vavasour commanded one of the three English regiments that reinforced the army of Sir William St Leger in February or early March 1642.
[11] On 13 April 1642 Vavasour fought under Murrough O'Brien, 6th Baron of Inchiquin, an Irish Protestant,[12] in the sally that lifted the siege by driving the rebels from their base at Rochfordstown.
[18] In the ensuing Irish Confederate Wars Vavasour was defeated on 4 June 1643 by James Tuchet, 3rd Earl of Castlehaven at the Battle of Cloughleagh and taken prisoner.
[19] On 15 September 1643 James Butler, 1st Marquess of Ormond, the Lord Lieutenant of Ireland signed a ceasefire, called the Cessation, with the Irish Catholic Confederation.