Jonathan Rhys Meyers was born as Jonathan Michael Francis O’Keeffe on July 27, 1977, in Dublin, Ireland. He was born prematurely with a heart condition and was baptized quickly for fear he would not live long. He spent several months in the hospital. He survived his first weeks and grew up in the city of Cork. He belonged to a working-class family and during his growing-up years worked as a farmhand. His mother was a voluntary worker and his father was a musician.
His mother, Mary-Geraldine, had three more children with Rhys Meyers' father, but their marriage ended by the time their oldest son was three. Two of the children went to live with their father, while Rhys Meyers and his brother grew up in a council flat, or public housing, in Cork. Both parents gave their own versions of the family history to British tabloid newspapers once Rhys Meyers became famous, and each denied reports that social services removed the children from their mother's home at one point. The actor admitted that he often went hungry as a child and sometimes resorted to stealing food, noting there were times when his mother spent her available funds on liquor. He once stated: "I love my family very much but once you're born, you're in the world on your own and I accepted that when I was very young."
His childhood included a spell in an orphanage, but as a teen, he befriended Anglo-Irish farmer Christopher Crofts with whom he went to live and who he refers to as "my gay dad".