The son of the Reverend Arthur Johnson, historian and chaplain of All Souls College, Oxford (and FA Cup winner in 1874 with Oxford University), and his wife, Bertha, Johnson was educated at Winchester College and New College, Oxford, graduating with a first in History in 1897. He was President of the Oxford Union. He joined the Scottish Education Department as a junior examiner and in 1910 transferred to HM Customs and Excise as Assistant Committee Clerk.