The Prefecture of Heraklion lies in the central eastern part of Crete. It borders the prefectures of Lasithi to the east and Rethymnon to the west, abutting the Cretan Sea in the north and the Libyan Sea in the south.

Heraklion Prefecture covers 2.641 square kilometers and has as its capital the City of Heraklion. In the census of 2001 the prefecture contained 26 municipalities, 194 municipal districts and 460 villages.

The prefecture terrain is mostly plain and semi- mountainous. So far it is the most economically developed prefecture of Crete and one of the most productive of Greece.