After receiving his primary education in Leghorn, Francesco Fanelli enrolled in the Art Institut "A. Passaglia" of Lucca, where he studied from 1893 to 1897 under the guidance of Michele Marcucci and Luigi Norfini.  After 1886 he took part in the circle of the young Leghorn painters, who were gathered around Silvestro Lega and, in Florence, he attended the meetings at the Trattoria Volturno of San Gallo Street, which, according to Signorini's evidence, was decorated by him with landscapes, portraits and animal shapes painted on the walls.

He participated in the discussion about the modern Tuscan painting and the necessity to modify the "macchia" in an impressionist direction; his painting however didn't undergo any fundamental transformation.  In 1888 he made his first appearance at the Florentine Promotrice with a study from nature still tied to the late-macchiaioli legacy.  Meanwhile he continued with his education, following Fattori's course at the Free School of Nude until 1895. Through his friend Ferruccio Pagni, who studied with him at Fattori's school, he discovered Torre del Lago, a still uncontaminated place of remarkable beauty, where he settled in 1893, founding the Club of La Bohème, a group of young artists close to Giacomo Puccini, famous resident of the area, which was made up of the same Pagni, Plinio Nomellini, Raffaele Gambogi, Angiolo and Lodovico Tommasi.

From 1894 he participated regularly in the exhibitions of the Promotrice Society of Florence with works which were inspired by the charming lake landscape. Towards the end of the century, he realized tempera decorations for Villa Orlando in Torre del Lago and for Villa Ginori in Piaggetta, skillfully combining naturalistic elements with floral and liberty patterns. In 1896 he exhibited at the first Triennale d'Arte of Turin, in 1897 at the III Triennale of Milan. In 1902, at the Quadriennale of Turin, he presented again paintings inspired by the landscapes of Torre del Lago and the wet dock of Viareggio; in the same year, until 1905, he was again at the Fine Arts Academy of Florence.

During the twenties, after the departure of Ferruccio Pagni for South America and the progressive decline of the bohèmien circles of Torre del Lago, he moved to Viareggio, where he took part in the birth of the literary coterie Gianni Schicchi, founded in 1919 in Giacomo Puccini's honour; and of the Zeteti Academy, where he met Moses Levy, Enrico Pea and the poet Elpidio Jenco.

He died during a stay in Bagno a Ripoli, close to Florence, on the 16th of July 1924.