John Brebner studied at Marischal College, Aberdeen, from 1848, obtaining the degree Master of Arts (MA) with distinction in 1852 and, as the best graduand of the year, received the gold medal of the city of Aberdeen. From 1851 to 1861 he taught at the Aberdeen grammar school while studying at the Aberdeen Free Church divinity hall. He was ordained a Presbyterian minister in 1861, though he never practised as such, and accepted a post as rector of the Albert academy in Burgersdorp, Cape Colony, where he arrived in October 1861. He soon learned Dutch and his academy became the outstanding school in the north-eastern districts of the Cape Colony. Early in 1869 Brebner became professor of classics at the newly established Gill College in Somerset East. During 1873-1874 he served as a member of the council of the University of the Cape of Good Hope (established in 1873). The university admitted him to the MA degree in 1877, on the basis of his degree from the University of Aberdeen. In January 1874, after the death of his wife the previous year, he accepted a post as inspector of schools in the Orange Free State (now the Free State). Here he played a major role in evolving a system of education adapted to the needs of a developing state and is still regarded as the founder of the Free State's educational system. Under his guidance the number of schools in the territory increased from 10 in 1874 to 199 in 1898, with corresponding increases in the numbers of pupils and teachers. He also played important roles in the economic, social, and religious life of the republic. In 1891 he became Superintendent of Education in the Free State. Two years later the University of Aberdeen awarded him an honorary doctorate.
Despite his busy life Brebner initiated regular meteorological observations in the Free State and passed them on to the Meteorological Commission of the Cape of Good Hope. His observations of maximum and minimum temperatures, atmospheric pressure, humidity, rainfall, wind and clouds at Bloemfontein started in April 1878 and were published with fair regularity in the Commission's annual reports for the next 20 years. He also persuaded friends and teachers in other towns to supply rainfall observations. Thus in 1881 rainfall data from Ladybrand, Boshof, Phillipolis and Kroonstad were supplied to him and passed on to the Meteorological Commission. In 1897 his weather station in Bloemfontein became a second order meteorological station, but that same year he handed responsibility for it over to Dr. W.R. Scott*.
Brebner was a foundation member of the Bloemfontein Debating Society (founded in 1877), which soon changed into the Bloemfontein Literary and Scientific Society. He also served on the first management committee of the National Museum of the Orange Free State in 1877. In January 1899 he resigned his post because of poor health and left South Africa. He returned towards the end of 1902, but died soon after his arrival in Cape Town.
Brebner married Jane Burnett in 1861. He married his second wife, Elizabeth Blackwell Laird, in 1877 and after her death in 1888 was married for the third time, to Elizabeth Helena Adelaide Van Andel.