The Boer Pony has similar origins to the Basuto pony, both having developed from the Cape Horse in the 19th century. During that time, however, the Boer Pony was also influenced by imported stock, such as Flemish, Hackney and Cleveland Bay horses, from which the Vlaamperd breed was developed. The Boer Pony did not have to survive such rough conditions as the Basuto pony did, and has consequently become a larger, better-developed animal. In the Boer wars, its great mobility and toughness helped the Boers move around and hold out against the British Empire for three years. Although thousands of horses were lost due to the harsh conditions. Top breeding horses were hidden away in the mountains so that the breed could be preserved.
Various attempts were made to form a Boerperd Society (in Afrikaans, 'boerperd' means 'farmer's horse', but can also be a reference to Afrikaners), and in 1973 the Boerperd Society of South Africa was formed. Today, Boerperds are found in isolated herds in the south-east Transvaal, northern Natal, eastern Free State and north-eastern Cape Province.