He was born at Great Torrington in Devon, and educated at Eton, where he was afterwards a renowned master, nicknamed "Tute" (short for "tutor") by his pupils.

Among his former pupils are numbered several statesmen of the period, including Lord Rosebery, Captain Algernon Drummond, Henry Scott Holland, Howard Overing Sturgis, Charles Wood, 2nd Viscount Halifax and Arthur Balfour.

Johnson was forced to resign from Eton at Easter 1872 after an "indiscreet letter" that he had written to a pupil was intercepted by the boy's parents and brought to the notice of the headmaster.

[5] Although it has been suggested that Johnson was a devoted paederast who numbered among his paramours Reginald Brett, the future Lord Esher,[6] the Oxford Dictionary of National Biography maintains that this cannot be proved and that "No one can be quite sure of the exact circumstances of his resignation," adding: "There is no question, however, that he was dangerously fond of a number of boys.

"[7] In dismissing Johnson, Hornby commented that it was not for committing acts of “immorality in the ordinary sense of the word”,[8] meaning sodomy in the euphemism of the era, and an alternative view of Johnson's dismissal is given by William C. Lubenow, who posits that Hornby "turfed out William Johnson and Oscar Browning because they were liberal reformers in a highly authoritarian institution ... [they] attempted to create a community where power and personality, desire and discipline, and love and learning were integrated.

"[9] Giovanni Costigan wrote in 1972, "In the century that has passed since then, no further light, incredible as it may seem, has been shed upon the subject [of Johnson's dismissal] ...

"[10] Johnson retired to Halsdon and changed his name on 17 October 1872 to Cory (the maiden name of his paternal grandmother) before emigrating for health reasons to Madeira in February 1878, where he married and had a son.