When the British Lions tour ended, Johnston, together with Thomas Crean, decided to stay on in South Africa. He played rugby for Transvaal and captained them in the Currie Cup. In 1899, at the start of the Second Boer War, again with Crean, he enlisted in the Imperial Light Horse and Johnston subsequently reached the rank of major. Johnston was already an experienced soldier, having previously served with the Royal Inniskilling Fusiliers between 1890 and 1894. He served in South Africa between 1899 and 1901 and was dangerously wounded during the Siege of Ladysmith. In October 1899, according to the Irish Times, the Imperial Light Horse particularly distinguished themselves in the Battle of Elandslaagte and it was during this engagement that Johnston, while still a captain, won his VC. The joint citation for him and Captain Charles Mullins reads:
On the 21st October, 1899, at Elandslaagte, at a most critical moment, the advance being momentarily checked by a very severe fire at point blank range, these two Officers very gallantly rushed forward under this heavy fire and rallied the men, thus enabling the flanking movement, which decided the day, to be carried out.[8]
Johnston was badly wounded and was nursed back to health by Crean. He travelled to London in early 1901, and both he and Mullins received the VC from King Edward during an investiture at Marlborough House 25 July 1901.[9] Johnston was awarded the Queen's South Africa Medal with clasps Elandslaagte and Defence of Ladysmith and the King's South Africa Medal with clasps South Africa 1901 and South Africa 1902 for his service in South Africa.[10][11] The location of his medals is unknown.[12]
In 1911 Johnston returned to Ireland and joined the General Prisons Board for Ireland (the G.P.B.). He was Commandant of the POW camp at Oldcastle 1914–15, and was appointed Governor of His Majesty's Convict Prison at Maryborough in 1915, before returning to Oldcastle in 1916. In 1918 he was appointed a resident magistrate. He later settled in Kilkenny, where he died. Conflicting sources give his date of death as either 1950[6][15] or 1970. He was buried in St. Mary's Churchyard, Inistioge, County Kilkenny.
In 2019 his story along with other Wanderers Victoria Cross recipients Thomas Crean and Frederick Harvey was told in a documentary entitled "Mark Our Place" directed and Produced by Ashley Morrison.
^A Victoria Cross is displayed at the Light Horse Bar at The Saturday Club in Kolkata, India but this is not confirmed to be either a genuine Victoria Cross or that it was awarded to Johnston. Reference works such as the VC and GC Association three volume work The complete Victoria Cross and George Cross published in 2013 and online sites such Iain Stewart’s Victoria Cross website (Archived 10 August 2016 at the Wayback Machine) have been unable to confirm the location of the VC.
^"Victoria Cross". British Military & Criminal History 1900 to 1999. Archived from the original on 3 March 2017. Retrieved 2 March 2017.