Jackson's father was of English descent, and his mother was of Welsh extraction.
John Hughlings Jackson was born on April 4, 1835, in Providence Green, Green Hammerton, near Yorkshire, England. His father, Samuel, was a yeoman who owned and farmed his land; his mother was the former Sarah Hughlings, the daughter of a Welsh revenue collector. She died just over a year after giving birth to Jackson. There were three sons and a daughter besides him; his brothers emigrated to New Zealand, and his sister married Doctor Langdale.