P. J. was the youngest of five children born to Irish Catholic immigrants Patrick Kennedy (1823–1858) and Bridget Murphy (1821–1888), who were both from New Ross, County Wexford, and married in Boston on September 26, 1849. The couple's elder son, John, had died of cholera in infancy two years before P. J. was born. Ten months after P. J.'s birth, his father Patrick also succumbed to the infectious cholera epidemic that infested the family's East Boston neighborhood. As the only surviving male, P. J. was the first Kennedy to receive a formal education. His mother Bridget had purchased an East Boston stationery and notions store where she had worked. The business took off and expanded into a grocery and liquor store.