Fattori was born in modest circumstances in Livorno. His early education was rudimentary and his family initially planned for him to study for a qualification in commerce, but his skill in drawing persuaded them to apprentice him in 1845 to Giuseppe Baldini (born 1807- ?), a local painter of religious themes and genre subjects. The following year he moved to Florence where he first studied under Giuseppe Bezzuoli and, later in the year, at the Accadèmia di Belli Arti. At that time, however, his energies were directed less toward the study of art than to reading the historical novels (especially those with medieval themes) of such authors as Ugo Foscolo, Francesco Domenico Guerrazzi and Walter Scott.
In 1848 he interrupted his studies and participated as a courier, distributing leaflets for the Partito d'Azione, in the democratic anti-Austrian movement during the revolutionary years of 1848-1849. However, his family prevented him from joining the army. In 1850 he resumed his studies at the Accademia in Florence. He made it a habit to note all his observations in small notebooks that he always kept with him, illustrating with innumerable sketches. Some of his later etchings were based on these observations.