Originally preceded by a wooden bridge, the Pons Aemilius was the first of many stone bridges constructed in Rome. It was designed between 179 BC and 151 BC. The bridge connected the central part of the city to the neighborhood of Trastevere, just south of Tiber Island.

Initially, only the pylons were made out of bricks. However, in 142 BC the original wooden arches were replaced by stone. The bridge was repaired several times over the centuries, most notably by Emperors Augustus in 12 BC and Probus in 280 CE.

With the fall of the Roman Empire, repairs became less frequent and multiple floods, especially those of 1230 and 1422, greatly damaged the structure. In 1552, the arches were replaced, yet, five years later, they were heavily damaged by another flood. A final renovation effort occurred between 1573 and 1575, but in 1598 the bridge was damaged again by floodwaters, which destroyed three of the six arches. The bridge was then abandoned and became known as "Ponte Rotto" ("Broken Bridge").

In 1853, the three remaining arches were connected to the mainland on both sides with an iron footbridge. This new iron structure weakened the original stone one. In 1887, the new footbridge was demolished along with two of the three arches to make room for a new bridge, Ponte Palatino. Today, only one 16th-century arch remains, resting on the original 2nd-century-BC pylons.