Manuel John Johnson was educated at the military college at Addiscombe, near London, and in 1821 entered the St Helena Artillery (of the English East India Company) with the rank of lieutenant. He became an aide-de-camp to General Alexander Walker, who supported his interest in astronomy and induced the East India Company to establish an astronomical observatory on the island. Johnson was put in charge of the project and to obtain advice on the construction of the observatory visited His Majesty's Astronomer at the Cape of Good Hope, Reverend Fearon Fallows*, from 29 December 1825 to 5 March 1826. At that time the Royal Observatory building was under construction near Cape Town, while Fallows made observations at his temporary observatory in Kloof Street. Fallows instructed him in observational techniques with the altitude and azimuth circle and a portable transit instrument, and the two became firm friends. Johnson took a copy of the plans of the Royal Observatory back to St Helena, where he supervised the building of an observatory on Ladder Hill, completed in March 1828. He returned for a second visit to the Cape from 12 September 1828 to 7 March 1829, when the Royal Observatory's instruments were being installed. A function to celebrate the laying of the last stone of the mural circle pier was held on 29 October 1828. Among the guests were Johnson, Fallows, John Skirrow*, Captain W. Ronald*, the Governor (Sir Lowry Cole) and the Colonial Secretary (John Bell). During this second visit Johnson assisted Fallows in conducting pendulum experiments to measure the local strength of the earth's gravitational attraction.
Johnson began observing on St Helena in November 1829, having installed a transit instrument and mural circle. Based on his star observations up to April 1833 he published A catalogue of 600 principal fixed stars in the Southern Hemisphere (London, 1835) for which he was awarded the gold medal of the Royal Astronomical Society in 1835. Other observations were published in the form of papers on the tides at St Helena (1829), transits of the moon (1833), Mars at its opposition in 1832 (1833), and the solstice of June 1832 (1833). In the course of his work he found that the star Alpha Centauri had a large proper motion (change of position on the celestial sphere over time), implying that it was relatively close and hence a good candidate for the measurement of its parallax (minute changes in position owing to the annual movement of the earth around the sun, and an indication of the star's distance). He wrote to His Majesty's Astronomer at the Cape, Thomas Henderson*, early in 1833 to inform him of this finding. In June that year Henderson, on his way back to Britain, visited Johnson on St Helena. Henderson had made a large number of observations of Alpha Centauri while at the Cape and used these to determine the star's parallax. It was one of the first such measurements to be published.
Johnson was retired when the English East India Company handed St Helena over to the British government in April 1834. Settling in Oxford he continued his studies and was awarded the degrees Bachelor of Arts (BA) in 1839 and Master of Arts (MA) in 1842. Around 1839 he was appointed Radcliffe Observer, that is, director of the Radcliffe Observatory at Oxford, a post he held until his death in 1859. Although the observatory had been founded in 1771, no observations made there had been published by the time of his appointment. He initiated systematic observations of star positions there, using a transit instrument and a mural circle, leading eventually to the publication, shortly after his death, of The Radcliffe catalogue of 6317 stars, chiefly circumpolar... (Oxford, 1860). His re-measurement of the positions of stars that had been observed 40 years earlier furthermore enabled him to determine their proper motions. In the 1850's he published a number of papers, four of them on his observations of some of the minor planets. During his term of office he produced 18 volumes of Radcliffe observations, re-equipped the observatory and expanded the meteorological observations made there. He was elected a Fellow of the Royal Society of London in 1856 and served as president of the Royal Astronomical Society during 1857-1858. He died of heart disease at Radcliffe observatory. Years later his collection of books and illuminated manuscripts, described as "small but extremely choice" was sold by auction.