Boarstall was an important site during the British Civil War. It was the centre of heavy fighting, changing hands between the Royalists and the Parliamentarians three times. Whilst Oxford, about 9 miles W.S.W. of Boarstall, was a Royalist stronghold, Aylesbury, about 16 miles E, was held by the Parliamentarians.

The Royalists set up a series of garrisons around Oxford, and Boarstall was one of the larger of these, near enough to Oxford to help with the protection of the City and near enough to Aylesbury to cause severe problems for the Parliamentarian garrison there. Yet the owner of Boarstall, the widowed Lady Penelope Dynham, was not a natural Royalist, and her son-in-law, Stephen Soame, was an active Parliamentarian.

In 1643, the Royalists built defences at Boarstall. Prince Rupert ordered the garrison to strengthen the fortifications in February 1644.

In March 1644, the King ordered Sir William Campion, Boarstall's garrison commander, to send "the two brass pieces" (i.e. cannon) at Boarstall to Oxford, so removing their chief means of defense. Not long afterwards, the Royalists decided to abandon their smaller garrisons, such as Boarstall and Reading. The Parliamentarians quickly took possession of Boarstall unopposed and caused as many problems for the Royalists at Oxford as the latter's skirmishing parties had previously caused for the Parliamentarians at Aylesbury. Realising their mistake, the Royalists decided to recapture Boarstall. Colonel Sir Henry Gage, with three pieces of cannon, a troop of horse and a party of infantry, recaptured it on 12th June 1644, having taken the church first and "then battered the house with cannon". The Parliamentarians, under Sir William Waller, tried to recapture Boarstall a month later but failed.

In December 1644, Colonel Sir William Campion was ordered by the King to demolish the church and adjoining houses and trees and to use the latter to make pallisades. Campion, perhaps not wishing to alienate the locals any more than was really necessary, only removed some houses and did not demolish the church.

After a failed attack by his second-in-command, General Philip Skippon, General Sir Thomas Fairfax, head of the Parliamentarian New Model Army, approached Boarstall on Sunday 1st June 1644. They attacked Boarstall with a mortar on Monday and shot 6 "Granadoes" at the house. They stepped up the pressure on Tuesday and Wednesday, the Royalist newspaper of the time, the "Mercurius Aulicus", reporting that the Parliamentarians shot Cannon "so thicke as not easily numbered, besides volleies [sic] of musketeirs [sic]". The Royalists did not respond very much, fooling the Parliamentarians into thinking that many of the garrison of the house had been killed so that Fairfax demanded their surrender. Campion, the Royalist commander, requested a pass to Wallingford for his pregnant wife which was granted. He then informed Fairfax that they intended to fight on. The Parliamentarians decided upon a full assault on the house, which took place at about midnight. They bombarded Boarstall with 8 cannon, firing about 250 shot, and 46 mortars. The rebels used 120 scaling ladders but the Royalists fired case shot and muskets "so thicke [sic] upon them" that they withdrew, leaving all their ladders behind. Fairfax's army totalled 1200 men, the Royalists claiming that they had killed some 300 of these and reporting that the Parliamentarians admitted to 120 deaths. The Royalists only lost one man from their small garrison (probably less than 100 men).

Only then did the Royalists complete the demolition of the centre of the village, leaving just Boarstall House, its fortified gatehouse (now known as Boarstall Tower) and the adjacent Elizabethan stable block and farmhouse (now Tower Farmhouse), presumably required for the garrison. Because it was a fairly substantial building, demolition of the church was not completed until towards the end of July.

The fortifications were considerably strengthened yet again and allowed Boarstall to withstand a siege of nearly 10 weeks in 1646. Sir William Campion only surrendered, on 10th June, when he heard that Oxford, the last outpost of the King, was about to surrender. The surrender of Boarstall was watched by several hundred spectators. Campion and his men were allowed to leave with their colours flying and heads high.

Despite the fierce fighting, there is little serious cannon fire or other damage visible on the Tower today. The only obvious sign of cannon damage is on the front of the Tower, above the entrance. Yet we know that the Parliamentarians fired from 8 cannon in their attack in 1645 and presumably had several cannon when they beseiged the Tower for ten weeks in 1646. Although there are some signs of repair at the front, these only cover a small area. The rest of the Tower looks totally undisturbed. If this was as the result of high quality restoration, why were some areas left unrestored or repaired rather poorly? A logical conclusion might be that the Parliamentarians were extremely bad shots but would they have wasted 250 canon balls? It seems unlikely. The gun emplacements were on the side of Muswell Hill, on the other side of the B4011, the road from Thame to Bicester. Given that large amounts of musket shot were found to the S.E of the Tower, in the field on the other side of the road, presumably this is the place from which the infantry attacked.