The museum is born in 1808 as the Gallery annex of the Academy of Fine Arts ("Accademia di Belle Arti"), founded from the old Clementine Academy. The core of the collection, from the Institute of Science, is enriched by the addition of a thousand of paintings from the abolition of male e female convents, churches, guild residences and religious educational institutes, due to the entrance of Napoleon French troops between 1797 and 1810.

The Pinacoteca saw a huge increase of extension both in space and artworks, due to the new abolitions made by the new Italian State, but also by new donations.

The major extensions was made in 1914/1920, when an entire wing was constructed (work of the Architect Edoardo Collamarini, under the direction of Francesco Malaguzzi Valeri), and in the 60s and 70s, with the realisation of the large Renaissance hall and the restructuring of the entrace hall with the two-flight staircase made by the Architect Leone Pancaldi under the direction of Cesare Gnudi, under the dome with the St. Ignatius Glory" of the Jesuit painter Giuseppe Barbieri.

The recommended itinerary starts with the expressive strenght of the Bolognese and Emilian artists of the XIII and XIV centuries, such as Vitale da Bologna, the Master of Bologna Polyptychs, and SImone dei Crocefissi, not to mention the considerable exemple of the Giotto polyptych. For this period of the Bolognese art is important the room which hosts the frescoes from the S. Maria di Mezzaratta church, reassembled according to the original architectural structure.

The Renaissance is featured by the Ferrarese Francesco del Cossa with his "Merchants Altarpiece" and Ercole Roberti with a small fragment depicting the Magdalene, from the Garganelli chapel of the St. Peter church, and by the Bolognese Francesco Francia, with several Altarpieces.

Starting from the Raphael's masterpiece ’”Extasis of St. Cecily” the itinerary reaches, after the Parmigianino painting of St. Margaret Altarpiece and the Passerotti - to the Reform of the late XVI century, with the work of the Carracci, among which we can stress the importance of the “St. Jerome Last Communion” by Agostino, the “St. Louis Altarpiece” by Annibale, the ’”Annunciation” and the “Bargellini Madonna” by Ludovico.

Then you can find the masterpieces of the Emilian Baroque, with the Guido Reni artworks, the “Massacre of the Innocents"  and the so-called “Plague Altarpiece”; the three exceptional Domenichino Altarpieces  depicting "The St. Agnes Martyrdom", the "Rosary Madonna" and the "St. Peter Martyr"; the Francesco Albani "Baptism of Christ", the Alessandro Tiarini “Entombment of Christ”, “St. Sebastian cured by Irene” and the Guercino "St. William receiving the Cow" .

The itinerary ends with the 18th century, with its various aspects - sometimes popular, sometimes aristocratic - of Giuseppe Maria Crespi (with his “Farm scene” and the "Self-Portrait"), Donato Creti (the two "Allegorical Tombs") and of the Gandolfi brothers, Gaetano and Ubaldo.