On 13 August 1898, John Lane married Annie Philippine King, the widow of Tyler Batcheller King and the daughter of Julius Eichberg. Annie Lane was author of To Thee, O Country (national hymn) and of the books Brown's Retreat, Kitwyk (published by John Lane in 1903), The Champagne Standard, Talk of the Town and According to Maria. John Lane died of pneumonia on 2 February 1925 at his London home, 8 Lancaster Gate Terrace, Bayswater, London. He was cremated at Golders Green, and his ashes were interred at St Nectan's Church, Hartland, Devon. His nephews, Allen, Richard and John, founded Penguin Books.
In the churchyard of St Nectan's, Stoke, near Hartland in Devon, there is a stone seat commemorating various members of the Lane family.