Construction of the tower occurred in three stages over 199 years. On 5 January 1172, Donna Berta di Bernardo, a widow and resident of the house of dell' Opera di Santa Maria, bequeathed sixty soldi to the Opera Campanilis petrarum Sancte Marie. The sum was then used toward the purchase of a few stones which still form the base of the bell tower.

On 9 August 1173, the foundations of the tower were laid. Work on the ground floor of the white marble campanile began on 14 August of the same year during a period of military success and prosperity. This ground floor is a blind arcade articulated by engaged columns with classical Corinthian capitals.

The tower began to sink after construction had progressed to the second floor in 1178. This was due to a mere three-meter foundation, set in the weak, unstable subsoil, a design that was flawed from the beginning. Construction was subsequently halted for almost a century, as the Republic of Pisa was almost continually engaged in battles with Genoa, Lucca, and Florence. This allowed time for the underlying soil to settle. Otherwise, the tower would almost certainly have toppled.

On 27 December 1233, the worker Benenato, son of Gerardo Bottici, oversaw the continuation of the tower's construction.

On 23 February 1260, Guido Speziale, son of Giovanni Pisano, was elected to oversee the building of the tower.

On 12 April 1264, the master-builder Giovanni di Simone, the architect of the Camposanto, and 23 workers went to the mountains close to Pisa to cut marble. The cut stones were given to Rainaldo Speziale, worker of St. Francesco.

In 1272, construction resumed under Di Simone. In an effort to compensate for the tilt, the engineers built upper floors with one side taller than the other. Because of this, the tower is curved.

At least four strong earthquakes hit the region since 1280, but the apparently vulnerable Tower survived. The reason was not understood until a research group of 16 engineers investigated. The researchers concluded that the Tower was able to withstand the tremors because of dynamic soil-structure interaction (DSSI): the height and stiffness of the Tower, together with the softness of the foundation soil, influence the vibrational characteristics of the structure in such a way that the Tower does not resonate with earthquake ground motion. The same soft soil that caused the leaning and brought the Tower to the verge of collapse helped it survive.

Construction was halted again in 1284 when the Pisans were defeated by the Genoans in the Battle of Meloria.

The seventh floor was completed in 1319.

The bell-chamber was finally added in 1372. It was built by Tommaso di Andrea Pisano, who succeeded in harmonizing the Gothic elements of the belfry with the Romanesque style of the tower.

Between 1589 and 1592, Galileo Galilei, who lived in Pisa at the time, is said to have dropped two cannonballs of different masses from the tower to demonstrate that their speed of descent was independent of their mass, in keeping with the law of free fall.

There are seven bells, one for each note of the musical major scale. The largest one was installed in 1655.

Numerous efforts have been made to restore the tower to a vertical orientation or at least keep it from falling over. Most of these efforts failed; some worsened the tilt. On 27 February 1964, the government of Italy requested aid in preventing the tower from toppling. It was, however, considered important to retain the current tilt, due to the role that this element played in promoting the tourism industry of Pisa.

The tower and the neighboring cathedral, baptistery, and cemetery are included in the Piazza del Duomo UNESCO World Heritage Site, which was declared in 1987.

after more than two decades of stabilization studies and spurred by the abrupt collapse of the Civic Tower of Pavia in 1989. The bells were removed to relieve some weight, and cables were cinched around the third level and anchored several hundred meters away. Apartments and houses in the path of a potential fall of the tower were vacated for safety. The selected method for preventing the collapse of the tower was to slightly reduce its tilt to a safer angle by soil removal 38 cubic meters (1,342 cubic feet) from underneath the raised end. The tower's tilt was reduced by 45 centimeters (17.7 inches), returning to its 1838 position.

The tower was closed to the public on 7 January 1990.

After a decade of corrective reconstruction and stabilization efforts, the tower was reopened to the public on 15 December 2001 and was declared stable for at least another 300 years. In total, 70 metric tons (77 short tons) of soil were removed.

After a phase (1990–2001) of structural strengthening, the tower has been undergoing gradual surface restoration to repair visible damage, mostly corrosion, and blackening. These are particularly pronounced due to the tower's age and its exposure to wind and rain. In May 2008, engineers announced that the tower had been stabilized such that it had stopped moving for the first time in its history. They stated that it would be stable for at least 200 years.