In ancient times, Tokushima City belonged to a region known as Myōdō-gun. In the first wave of government consolidation following the abolishment of the fiefdom system and construction of prefectures in 1871, it became known as Myodo Prefecture. At the time, it included the Awa region to the south and the Awaji Island regions as well. In 1873 it further incorporated the region currently occupied by Kagawa Prefecture in its borders.

In the second wave of government consolidation, on September 5, 1875, the Sanuki Region separated to form the modern day Kagawa Prefecture. On August 21, 1876, Awaji Island separated to join Hyogo Prefecture and the Awa region separated to form Kochi Prefecture.

On March 2, 1880, Myodo Prefecture fully separated from Kochi Prefecture to be inaugurated as Tokushima Prefecture.

The Sanuki Mountains run along the northern border of the prefecture.

As of April 1, 2012, 9% of the total land area of the prefecture was designated as Natural Parks, namely the Setonaikai National Park; Muroto-Anan Kaigan and Tsurugisan Quasi-National Parks; and Chūbu Sankei, Dochū-Kōtsu, Hashikura, Higashi Sankei, Okumiyagawa-Uchidani, and Ōasayama Prefectural Natural Parks.

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