Quillinan was born in Oporto, Portugal, on 12 August 1791. His father, also named Edward Quillinan, was an Irishman of a good but impoverished family who had become a prosperous wine merchant at Oporto. In 1798, the younger Quillinan left Portugal to be educated at Roman Catholic schools in England; his mother (whose maiden name was Ryan) died soon after. After returning to Portugal, Quillinan worked in his father's counting-house, but this arrangement ceased upon the Invasion of Portugal under Jean-Andoche Junot in 1807, which obliged the family to seek refuge in England.