Guybon D. Atherstone was the eldest child of the eminent Dr W.G. Atherstone* of Grahamstown. He was educated at St Andrew's College, Grahamstown, and qualified as an engineer at King's College, London. In 1872 he published an article on "Railway extension" in the Cape Monthly Magazine (Series 2, Vol. 4, pp. 344-351), dealing mainly with raising capital for further railway construction in the Cape Colony. He joined the Cape Government Railways as assistent engineer, construction, in 1873 and was promoted to district engineer in 1876. After serving as district engineer of the Kowie railway from 1880 he left the railways in July 1881, but was re-appointed the same year as district engineer of the Colesberg survey (1881) and Colesberg extension (1882). He was thereafter employed in the midlands railway system (1884), at Touwsrivier (1885), on the Indwe and Victoria West surveys (1888), the Norval's Pont construction (1889), and the Bloemfontein Vaal River line survey (1890). In April 1891 he was appointed district engineer at Bloemfontein, where he remained until 1897.
In 1899 Guybon Atherstone donated about 30 maps to the Albany Museum. These maps were mainly of historical interest and had probably belonged to his father, who had died the previous year. Years earlier, in 1882, he had shot and donated a pair of black eagles from Noupoort to the museum.
Atherstone was an early member of the Cape Society of Civil Engineers (founded in 1902), which listed his address as the survey camp at Sandflats in 1903, but thereafter as the Albany Club in Grahamstown. He was also a member of the (British) Institution of Civil Engineers. He briefly became a member of the South African Association for the Advancement of Science in 1907-8 and served on its committee for Section B (which then included engineering), and was therefore involved in planning the association's 1908 meeting in Grahamstown.
Atherstone was married to Antoinetta, born Richardson.