:Not to be confused with Saint Francis Borgia nor Francisco de Borja Echeverría, nor with Francisco Lloris y de Borja.
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Fernando was the son of Juan de Borja y Castro, I Count of Mayalde and his wife, Francisca de Aragón y Barreto, Countess of Ficalho, and paternal niece of Francisco de Borja who was also Fernando's paternal grandfather.
El Colegio del Príncipe, established by Royal Decree of King Carlos III after the expulsion of the Jesuits, was the former "college of chiefs" of the native nobility, created during the reign of Viceroy Francisco de Borja y Aragón Príncipe de Esquilache in Lima.