The earliest record of settler activity in the Naauwpoort area dates back to 1803 when one J.P. van der Walt was resident on the farm Caroluspoort. The district was visited from time to time by wandering trekboere or nomadic farmers over the years. The railway line from Port Elizabeth reached the Carlton Hills to the south of Noupoort by 1881 and with the construction of the railway through the thick reeds and bush of the Poort there was the ever-present danger of marauding lions. The development of the railway line linking Port Elizabeth and De Aar in the 1880s necessitated the establishment of a railway station and junction. In 1884 Hartebeeshoek Farm was bought from its owner Barend Kruger and the new railway station of Naauwpoort came into existence. Over time a village developed around the railway station and eventually Naauwpoort achieved municipal statues in 1942. The town was eventually renamed Noupoort in 1963 by simply changing the Dutch name to Afrikaans.

Noupoort was garrisoned during the 2nd Anglo Boer war to protect the important railway junction from the invading Boer Commandos. From November 1899 Boer Commandos invaded the Cape Colony from the Orange Free State in order to subvert the British and Colonial Forces advance towards Bloemfontein and Kimberley and in an abortive attempt to get the local Dutch speaking communities of the Cape Colony to rise up in revolt against the Colonial authorities. In the vicinity of Noupoort both Colesberg and Venterstad were occupied by the Boer Commandos. On the 20th November 1899 Major General John French arrived in Noupoort to prepare for the advance on the occupying Boer forces in Colesberg. In advance of his attack the Boers withdrew from Colesberg on 25 February 1900. A significant military hospital was established in Noupoort to care for the British sick and wounded and a small number of Boer Prisoners of War were also kept captive in a stockade.

The St Agnes Anglican church was designed by a railway engineer in commemoration of the fallen British soldiers. It was built in 1901 by British troops, of which some were stonemasons, who were stationed at Noupoort at the time. The British troops were repatriated before they could complete the church. The British military camp and hospital contributed considerably to the completion and membership of these churches during the 2nd Anglo Boer War. After the British troops left Noupoort at the conclusion of hostilities the number of members dwindled significantly and the Methodist and Presbyterian churches amalgamated in the Presbyterian Church Building. The Methodist Church was first used as classrooms during the period between 1916 and 1918 after standing empty for a number of years. A British military museum is now housed in the old Anglican Church building.

Many countries and organisations similar to the Red Cross sent equipment and personnel to South Africa during the 2nd Anglo-Boer War. Among these was a group of Scots from Edinburgh who collected £12,000 to establish and staff a hospital. They embarked on the SS Briton from the United Kingdom and arrived in Cape Town on 10 April 1900. There was no transport to take them inland, so they did not disembark, but sailed on to Port Elizabeth. There they found no suitable accommodation for the nurses, so on 17 May 1900 these women were sent on to Noupoort where they joined the Number 26 General Hospital. The appalling health conditions had devastating consequences within three weeks of their arrival. Sister Mary Boyd, the sister of physician Dr Francis D. Boyd, was struck down by dysentery. Nothing could be done to help her and she died four months later. One of the medical orderlies, William Dick, also died of typhoid. Interestingly Boer Commandant Gideon Scheepers was nursed back to health at the Noupoort Hospital after his capture, before being sent to Graaff-Reinet for trial and subsequent execution.

The extraordinary and unique Noupoort Blockhouse was probably adapted from an existing structure, most likely a windmill, to serve as a lookout and fortified point for the British soldiers stationed at Noupoort. Very difficult to access today, as the entrance is seven metres above ground level, the structure was adapted for war conditions with five steel loopholes set vertically and a further fifteen loopholes set horizontally at the top of the structure. The loophole plates are unusual in that they are mounted on the outside wall face and not in the middle of the wall layer as is customary, and the apertures are much larger than usual. The building is eight metres in diameter at the base tapering to about seven metres at the top and the blockhouse is some seven metres tall.

In the final year of the war and in an attempt to disrupt the British war effort there were multiple Boer Commando raids on the Cape Colony. On 17 December 1901 Commandant Pieter Kritzinger, harried by Colonial forces, was forced to cross the railway line between Hanover Road and Taaiboschfontein to the south of Noupoort in full view of the blockhouses. During the skirmish Kritzinger was badly wounded and was transported by the British to the hospital in Noupoort. He was later tried by a British military court for war crimes, but was acquitted. The garden of remembrance in the Noupoort cemetery contains the graves of many British and Colonial troops who were killed in action in the area.