Shackleton was a militiaman; the 3rd Royal Irish Fusiliers were embodied on 14 May 1900. Shackleton did not serve with them during his time in South Africa. He was attached to 3rd Royal Munster Fusiliers, per the medal roll. This is confirmed in the regimental records.
3rd Battalion, Royal Munster Fusiliers, arrived at Table Bay on 19 March 1900. The companies were then split up around Stormberg at the end of the month, and by 15 May the majority of the battalion was guarding prisoners of war at Frere Camp, near the Orange River. The battalion moved to Vryburgh on 7 August, where they built South Cork Fort. From there they were sent to enhance the Mafeking garrison, with their duties mostly being convoy escorts. Combat was in the form of occasional sniping Boers only. The battalion was moved back to Vryburgh in September, where they joined a column under General Henry Settle, which went about relieving garrisons, seeing more sniping and small-scale combat along the way; Schweizer Reneke on 22 September and Hoopstaad on 17 October. They subsequently reached Karripan and Christiana on 27 October, before occupying Bloemhoff. While on the way to join an operation against De Wet, the battalion was ambushed by Lemmer and Tolly De Beer while in camp. The Munsters lay flat on the ground and did not return fire, having twenty-four men wounded. Orders were subsequently cancelled and the battalion returned to Hoopstaad. They they shelled a lager with a howitzer, and used a combined force of maxims to attack Boers waiting by the riverbank to ambush cavalry as they watered their horses. After this the column moved to Boshof, attacking another small force of Boers, before moving on through Kimberley and then south of the Modder River. Having reached the Orange Free State at Ramah, the battalion left the column on 27 November and was split up to form several garrisons. In August 1901 the battalion was brought back together to be deployed along the railway line for its protection, garrisoning blockhouses.
The regimental records note that when the 1st Royal Munster Fusiliers left the area for Kimberley, they took 100 men from the 3rd as well, who had come out to South Africa with Captain R. C. Boyle in July 1900. I would speculate that Shackleton could be one of these men; he departed for Britain on board the "Dilwara" on 24 August. He had returned to the 3rd Royal Irish Fusiliers at Dublin in time to win the officers' donkey race on 2 October, and was promoted to lieutenant on 6 November. Still a lieutenant, he resigned his commission on 19 September 1907.