His parents were Flaín Muñoz and his wife Justa Fernández, daughter of count Fernando Bermúdez de Cea.
Jointly with his son, Flaín Fernández, he governed the city of León until 1038 when the kingdom was already under the control of King Sancho III of Pamplona.
He first appears in medieval charters in 999 when, jointly with his brother Munio, he confirmed a donation by the Bishop of León to the Monastery of Sahagún.
[c] However, at first, he accompanied the young monarch as evidenced in a donation made by Bermudo III in November 1028 to the Cathedral of Santiago de Compostela where he appears with other magnates confirming the royal charter.
Fernando Flaínez did not hand over the capital of the Kingdom of León to Ferdinand I until 1038 and kept all his honors and estates until his death, after 1049, the last year in which he appears in the charters of the Monastery of Sahagún.