The 1st Battalion sailed from Malta on 27th September 1899, landed at Cape Town on 21st October, and was sent to De Aar. After two days there they were taken to East London, and thence by steamer to Durban. Along with the 1st Inniskilling Fusiliers, 1st Connaught Bangers, and the 1st Dublin Fusiliers, they formed the 5th Brigade under Major General Hart, the Border Regiment taking the place of the 2nd Royal Irish Rifles, which had been left in Cape Colony. The work of the brigade is sketched under the Inniskilling Fusiliers, and that of the Natal Army under the 2nd Queen's.
At Willow Grange the battalion was in support.
At Colenso on 15th December 1899 the battalion was in support of the rest of the brigade in the attack near Bridle Drift. It lost 6 men killed, 3 officers and 42 men wounded. The battalion was specially mentioned by General Buller.
At Venter's Spruit the battalion was heavily engaged on 20th January, and between the 20th and 26th lost 1 officer and 7 men killed, and 4 officers and about 133 men wounded.
In the final effort to relieve Ladysmith the Imperial Light Infantry took the place in the brigade of the Border Regiment, which on the 27th, the day of the great assault on Pieter's Hill, was, along with the Composite Rifle Battalion, employed in keeping up a continuous long-range fire on the enemy's trenches from the hills south of the Tugela,—a fire which Mr Churchill and others said was very helpful to our troops engaged in the assault. Six officers were mentioned in General Buller's despatch of 30th March 1900, 3 non-commissioned officers were recommended for the distinguished conduct medal, and 3 others were mentioned in General Warren's despatch of 1st February 1900.
About the middle of April 1900 a division known as the Xth Division, under Sir Archibald Hunter, was brought round from Natal to Cape Colony. It consisted of Barton's Fusilier Brigade and Fitzroy Hart's brigade, now composed of the Somerset Light Infantry, which took the place of the Royal Inniskilling Fusiliers, the 1st Border Regiment, 1st Connaught Rangers, and 2nd Dublin Fusiliers. The division went straight to Kimberley, except the Somersets and this battalion, which were utilised in the operations for the relief of Wepener, which was accomplished about 24th April. The Border Regiment had some fighting about the 22nd and 23rd, losing 7 wounded. These battalions were now railed to the Transvaal western border. One wing of the Somersets was left at Vryburg; the rest of the brigade marched to Potchefstroom and Krugersdorp. The other wing of the Somersets and the 2nd Dublins went on to Heidelberg, while the 1st Border Regiment and 1st Connaught Rangers went to Irene and were posted east of that place under Mahon.
On 9th July General French, with Hutton and other troops, including those of Mahon, "engaged the enemy and pushed them back beyond Bronkhorst Spruit". On the 12th the Border Regiment, Connaught Rangers, and Royal Fusiliers marched back to Pretoria.
To clear the country north of Pretoria a column under Ian Hamilton was organised, which included an infantry brigade, consisting of the 1st KOSB, 1st Border Regiment, 2nd Berkshire, and 1st Argyll and Sutherland Highlanders. This column left Pretoria on 16th July; between that date and the 25th Ian Hamilton's force was on the left in a further advance eastwards to Balmoral, and then returned to Pretoria to operate north-west towards Rustenburg. They had some stiff fighting in hilly country (see 1st KOSB) The Border Regiment was left in the Megaliesberg; the remainder returned to Pretoria in August, very short of supplies. Meanwhile De Wet had crossed to the north of the Vaal. An attempt was made to surround him. The Border Regiment and some mounted troops were posted at Commando Nek with Baden-Powell. De Wet crossed the Megaliesberg range at Oliphant's Nek and paid a visit to Baden-Powell, sending a message asking surrender, which was politely rejected. Next day De Wet was hastening from the district pursued by Mahon.
In September 1900 the battalion was again in a column operating from Commando Nek under General Clements, his other troops being 2nd Northumberland Fusiliers, 2nd Worcesters, 2nd Yorkshire Light Infantry, the 8th Battery, and 900 mounted men under Ridley. The battalion was still under General Clements at the time of his defeat at Nooitgedacht on 13th December 1900, but was not present with him on that occasion, having been left to guard Krugersdorp.
About the end of December 1900 the battalion had some skirmishes in the Megaliesberg; they also fortified and held Breedt's Nek. The battalion was now under General Cunningham, and with him was engaged against Delarey at Middlefontein, 23rd to 25th January 1901, when the Border Regiment had 6 killed and 15 wounded. The battalion continued to operate in the South-West Transvaal. In April 1901 they were detailed to guard the Klerksdorp-Krugersdorp Railway. In September 1901 the battalion was in garrison at Potchefstroom—Colonel Ovens, who had been on sick-leave, rejoining at this time and being commandant of the town. In January 1902, after a visit from Lord Kitchener, the battalion built a line of blockhouses from near Ventersdorp to Lichtenburg so expeditiously as to gain a complimentary wire from Lord Kitchener. The battalion garrisoned this line till the end of the war. They claim that no Boers crossed it, although some thirty attempts were made.
In Lord Roberts' final despatch 11 officers and 16 non-commissioned officers and men were mentioned. Three officers and 3 non-commissioned officers and men were mentioned by Lord Kitchener in despatches during the later phases of the war, and in the final despatch the names of 3 officers and 3 non-commissioned officers were added.