Its building history involved some of the most prominent Italian architects of the 16th century, including Michelangelo, Jacopo Barozzi da Vignola and Giacomo della Porta.

When, in January 1534 Alessandro became Pope Paul III, the size of the palace was increased significantly and he employed Michelangelo who completed the redesigned third story with its deep cornice and revised the courtyard as well.

On the garden side of the palace, which faced the River Tiber, Michelangelo proposed the innovatory design of a bridge which, if completed, would have linked the palace with the gardens of the Vigna Farnese, Alessandro's holding on the opposite bank, that later became incorporated into the adjacent villa belonging to the Chigi family, which the Farnese purchased in 1584 and renamed the Villa Farnesina.

After Odoardo's death, Pope Alexander VII allowed Queen Christina of Sweden to lodge in the palace for several months, but she "proved a tenant from hell".

[7] After her departure for Paris, the papal authorities discovered that her unruly servants not only had stolen the silver, tapestries, and paintings, but also had "smashed up doors for firewood" and removed sections of copper roofing.

Carracci adopted the quadri riportati, which the ceiling is divided into units and turned it into a collection of framed paintings, along with the cast masks among the garlands, and carved putti, and sculptures supporting the central scene.

In Puccini's opera Tosca (1900), set in Napoleonic Rome, the heroine's confrontation with the malevolent chief of police, Scarpia, takes place in Palazzo Farnese.

The Palazzo Farnese houses the great scholarly library amassed by the Ecole Française de Rome, concentrating especially on the archeology of Italy and medieval Papal history.

The Ecole Française de Rome embarked on a massive project of publishing as much of the documentation of the constructing of the palazzo, its frescoes and furnishings, library and works of art, fully annotated and indexed.