Anderson was born at Edinburgh in 1850. His father was John Anderson, who was to become mayor of Christchurch and an influential businessman. His mother was Jane Anderson (née Gibson). The Andersons emigrated to Canterbury in New Zealand at the end of 1850 on , one of the First Four Ships, and settled in Christchurch. His parents, who had married in 1845, had previously lost two children during infancy and it is thought that this contributed to their decision to emigrate; John Anderson Jr. was their only child alive at that point. Another son, Andrew, was born in 1851.
