Inhabited since Etruscan times, when the local area was used as a granary for the thriving town of Vulci, the first documentary evidence dates back to the 8th century A.D. when there's mention of a certain Cellulis in a sale document in the Siena City-State archives.

The fortress was built in the 11th Century to hold back the Barbarians and Longobards. Over the centuries the town passed through many hands, local nobles, the Church, the city of Viterbo and even Tuscania (in 1254, with Canino). Then, in 1340, it became the property of the important Farnese family, under whom the town flourished and expanded. The Rocca Farnese that domninates the town was built during this period. Cellere, like several other towns in the area, was annexed to the Ducato di Castro in 1537 until it returned to the Church in 1649. During this period, thanks also to the innumerable debts incurred by the Farnese family, the town fell into disrepair. In 1788 it was handed by Pope Pius VI to the Marquis Casali Patriarca who retained it until the Risorgimento when it passed to the State.