A Chosen One was a Human child that Fairies protected up till a point where the child was taken to become a Fairy. The Fairies required these children to continue the existence of their race. The Fairies protected these children, sometimes by killing their attackers.
In 1909, one of Jack Harkness's soldiers accidentally killed a Chosen One in Lahore. In retaliation, the Fairies killed all his men, sparing only Jack.
In 2007, Torchwood Three was unable to stop the Fairies from claiming Jasmine Pierce as their Chosen One. (TW: Small Worlds)