The 2nd Battalion sailed on the Goorkha about 4th January 1900, and arrived at the Cape about the 25th. Along with the 2nd Norfolk, 1st KOSB, and 2nd Hampshire, they formed the 14th Brigade under Brigadier General Chermside, and part of the VIIth Division commanded by Lieutenant General Tucker. For the work of the brigade and division see notes under 2nd Norfolk Regiment.
The Lincolns had no very heavy fighting on the way to Bloemfontein. One officer was mentioned in Lord Roberts' despatch of 31st March 1900.
At Karee Siding the battalion was not heavily engaged. Their losses were 2 men killed and 1 officer and 4 men wounded.
After Pretoria was occupied the 14th Brigade was detailed to garrison the Boer capital and neighbourhood.
Early in July 1900 the post at Zilikat's Nek, Uitval's Nek, or Nitral's Nek, in the Megaliesberg Mountains, was taken over from Baden-Powell's force by a squadron of the Royal Scots Greys, five companies of the Lincolnshire Regiment, and two guns O Battery, RHA, the whole under Colonel H R Roberts. On 11th July the enemy in great numbers attacked the position, and "owing mainly to the defective dispositions of the commanding officer, the enemy gained possession of the pass and captured the two guns, almost an entire squadron of the Scots Greys, and 90 officers and men of the Lincolnshire Regiment, including Colonel Roberts, who had been wounded early in the day".
The battalion was present at the ceremony of proclaiming the annexation of the Transvaal in Pretoria on 25th October.
Seven officers and 13 non-commissioned officers and men were mentioned in Lord Roberts' final despatch.
In the later phases of the campaign the battalion furnished infantry for columns as well as doing garrison duty. In 1901 two companies were under Colonel Grenfell when he operated on the Pietersburg line.
The Mounted Infantry Company of the battalion did very excellent work in many districts, and gained no fewer than six mentions in Lord Kitchener's despatches during the war. In his final despatch 2 officers and 6 non-commissioned officers of the Lincolnshire Regiment were mentioned.