The 2nd Battalion was in Cape Colony when the war commenced. Major Pollock says that when he arrived at Queenstown, about 8th November 1899, the garrison there was a naval detachment with two 12-pounders and the "headquarters and four companies of the Royal Berkshire Regiment (which had been withdrawn from Stormberg) with the mounted infantry company of that excellent corps". In addition to these were some of the Cape Mounted Rifles and other local forces. At this time the other companies of the Berkshires were at Naauwpoort, west of Stormberg.
There was little fighting in Sir William Gatacre's district until he made his ill-fated attempt on the Boer position at Stormberg upon the night of 9th December 1899. The terms of Lord Roberts' criticism on Sir William Gatacre's despatch are within the recollection of all interested in the war (see covering despatch of February 1900). In his criticism on the action Major Pollock says, p 59, "The Berkshire Regiment, by whom the redoubts, now occupied by the Boers, at Stormberg had been built, and to whom every inch of the ground was familiar, were left at Queenstown instead of being employed to recapture the works which they had so unwillingly evacuated about a month previously". The folly of the proceeding would be ludicrous if the result had not been tragic. At Naauwpoort General French did not leave the battalion in the background. On 1st January 1900 a part of the Boer position at Colesberg was seized. In his despatch of 2nd February, General French says: "The attack and seizure of the hill, the position of which he knew well, was intrusted to Major F W N M'Kracken, Berkshire Regiment ... The attack was carried out in every detail as ordered. The four companies of the Berkshire Regiment rushed the hill most gallantly, driving off a strong picquet of the enemy". Henceforth these four companies were to have plenty of fighting. Daily a half of them were under fire, but always held their own. At the close of his despatch General French says: "To Major M'Kracken and the four companies of the Berkshire Regiment serving with this force is the successful attack on Colesberg on 1st January principally due. I cannot speak too highly of this officer's coolness, courage, and intrepidity, or of the gallantry and discipline displayed by his officers and men in making the night assault which he led so well. What in my opinion is worthy of even greater praise is the conduct this gallant regiment displayed in the tenacity with which they have held the position ever since, and the skill with which they have intrenched themselves against a constant fire from artillery and musketry".
These companies accompanied General Clements when he moved north, crossing the Orange River at Norval's Pont about 12th March. Marching via Fauresmith and Petrusburg, that general arrived at Bloemfontein about 2nd April.
The battalion took part in the operations for the relief of Wepener about 20th-23rd April, but had no serious fighting. During Lord Roberts' advance towards Pretoria they were chiefly employed guarding the line.
In the beginning of July the battalion joined a newly formed brigade under Brigadier General Cunningham, consisting of 1st KOSB, 1st Border Regiment, 2nd Berks, and 1st Argyll and Sutherland Highlanders. This brigade and other troops were put under Ian Hamilton, whom they accompanied to Bronkhorst Spruit. The force was then sent back to Pretoria, and thence towards Rustenburg, having a good deal of fighting north-west of Pretoria. On 2nd August, "on approaching Uitval Nek, Hamilton found it strongly held by the enemy, whom he engaged in front with a portion of Cunningham's brigade, while two companies of the Berkshire Regiment gallantly escaladed the steep cliff overlooking the pass from the east". Thereupon the enemy fled. The battalion's losses were 3 men killed, and 2 officers and 30 men wounded. Having returned to Pretoria, the column again went east, reaching Balmoral about 4th September.
Private William House gained the VC on 2nd August 1900 for going out under very heavy fire to bring in a wounded sergeant, he himself being wounded and refusing assistance as the fire was so intense.
Ten officers and 19 non-commissioned officers and men were mentioned in Lord Roberts' final despatch.
In December 1900 the battalion formed the garrison of various posts in the Wonderfontein-Pan district, and had fighting on many occasions.
When Dalmanutha was attacked early in January 1901 part of the Berkshire Regiment were in the garrison. They lost 1 killed and 4 wounded in repelling the attack.
The battalion long remained in the Eastern Transvaal, and in 1901 was the infantry of a column under Brigadier General Spens.
In September 1901 the battalion was back in Cape Colony operating under General French against Scheepers, and down to the close of the war they held a stretch of the railway between Beaufort West and De Aar.
During the war 2 officers and 2 non-commissioned officers gained mention by Lord Kitchener, and in his final despatch 4 officers and 10 non-commissioned officers and men were mentioned.