In the Civil War, he fought as a colonel on the King's side, raised a regiment at his own cost and commanded the successful defence of Basing House in Hampshire in 1643. On 28th December of the same year he was knighted. After Sir George Lisle's recall to the King's headquarters in Oxford in May 1645, Rawdon left Basing with a force of 50 horse and 450 foot soldiers to become Governor of Faringdon in Berkshire, a strategic point in the defensive ring around that city. With his Faringdon forces, he took part in a number of skirmishes at Highworth, Lechlade, Bampton and Radcot Bridge. In April 1646, these were followed by the Second Siege of Faringdon when Parliamentary forces infiltrated the western end of the town and set up a defensive earthwork. Rawdon's counter attack captured this, but his men suffered heavy casualties. A second push from the south was also stopped, but the enemy eventually managed to establish a gun battery in the east, commanded by Sir Robert Pye Junior, whose absent father usually resided at Rawdon's seconded headquarters, Faringdon House. There was a heavy bombardment against Rawdon's snipers up the church tower in an attempt to topple the steeple into the Royalist lines. Aware of the danger, Rawdon had it blown up to fall in the opposite direction; but, by this time, the colonel was sixty-three and seriously ill. He died at Faringdon House on 28th April 1646 and was buried with full military honours, including cannon and musket-fire, in the nave of Faringdon Church. The building took a direct hit from a 200-pound Parliamentary mortar shell shortly after the funeral had ended. 

In 1611, while a ‘clothworker of All Hallows Barking,’ Rawdon had married Elizabeth, daughter of Thomas Thorowgood of Hoddesdon in Hertfordshire. His son, Thomas, also fought as a colonel in the Royalist Army and, after the Battle of Marston Moor, found asylum in the Canary Islands. His nephew, Marmaduke Rawdon, the antiquary, lived in his house for some years from 1626.