John Scott Haldane was born in Edinburgh. He was the son of Robert Haldane and the grandson of the Scottish evangelist James Alexander Haldane. His mother was Mary Elizabeth Burdon-Sanderson, the daughter of Richard Burdon-Sanderson and the granddaughter of Sir Thomas Burdon.
His maternal uncle was the physiologist John Scott Burdon-Sanderson. He was the brother of Elizabeth Haldane, William Stowell Haldane and Richard Burdon Haldane, 1st Viscount Haldane.