He was a member of the Ernuszt noble family of Jewish origin, founded by his paternal grandfather, John I Ernuszt. Francis was the eldest son of John II Ernuszt, Ban of Croatia, Dalmatia and Slavonia and his second wife, Princess Margaret of Sagan (Żagań), daughter of Jan II the Mad. He had a younger brother, John III. His uncle was Sigismund, Bishop of Pécs. Through his mother, he was also a half-brother of John Bánffy, Palatine of Hungary, author Katalin Bánffy and Margit Bánffy, spouse of John II Both de Bajna (killed in the Siege of Belgrade in 1521), later John Dombai. After his mother's death, his father married Barbara Ország. From this marriage, Francis also had two half-brothers, Farkas and Caspar, who was the last male member of the Ernuszt family.