Founded in 1257 under Pope Alexander IV, thanks to the work of the Franciscan monk and Apostolic Penitentiary Mansueto Tanganelli, the Pisa hospital incorporated various church and monastery hospitals. At first called the "New", "Pope Alexander" or "the Misericordia" hospital, it later assumed the name of the nearby church of Santa Chiara, and its administration, granted independence, was entrusted to Augustinian monks.

Between the 13th and the 15th century, 44 hospitals are recorded as existing in Pisa. Among these were the hospitals of San Vito, Capitolo, San Pietro in Vincoli, San Zeno, Santa Lucia dei Ricucchi, San Matteo, San Paolo a Ripa d'Arno, San Sepolcro, the lepers’ hospital of Stagno, that of Santa Caterina, the orphans’ hospital "della Pace", the "San Francesco" hospital, a poor women’s hospital, one for poor priests, and a mariners’ hospital.

During the period of the Medicean Grand Duchy, the Santa Chiara Hospital passed under the jurisdiction of the Hospital of Santa Maria Nuova in Florence, and then became independent again in 1771. Significant enlargement took place under the government of Peter Leopold, and again in the 19th century, in connection with evolution of the medical and anatomical sciences at the University of Pisa.

An ancient 16th century pharmacopoeia documents the existence of a "spezieria". Starting in the 17th century, the pharmacy was closely linked to the activity of the Giardino dei Semplici (medicinal herb garden) and its Foundry. Of its history today there remains only a sign and a few ceramic vases from its antique furnishings.