John Laughton was born in Liverpool on 23 April 1830, son of a Master Mariner. He was educated at the Royal Institution School, Liverpool and Caius College, Cambridge, where he read mathematics and graduated as a wrangler in 1852. He entered the Royal Navy as an instructor, joining his first ship, Royal George, in 1853, serving in the Baltic during the Crimean War. In 1866 he went ashore to teach at the Royal Naval College at Portsmouth, moving with the College to Greenwich in 1873, becoming Head of the Department of Meteorology and Marine Surveying.