John Holt, the eldest son of Thomas Godfrey Holt, was born in the village of Garthorpe, in Lincolnshire, on the 31st October, 1841. He was educated at the local village school which he left at the age of fourteen to enter the employ of his grandfather, Thomas Holt, and he went to sea on a schooner owned by his grandfather, which plied between Goole and London and the Northern French ports, carrying coals, cement, and tiles. The name of the schooner was the Thomas Holt. He apparently did not find this employment to his liking, and on the 1st July, 1857, his father signed an agreement with William Laird, of Messrs. W.H. Laird, Coal Dealers, Castle Street, Liverpool, to employ him as an apprentice for a period of five years.

William Laird was one of the well-known family of Lairds, who had shipping and shipbuilding interests in Liverpool, and was a brother of Macgregor Laird, the explorer. In Laird's office together with John Holt was Alfred Jones who later became Sir Alfred Jones, of West African fame.