Agioi Deka was once part of ancient Gortyn. The Roman cemetery may have been located here. When constructing the modern houses, the residents reused building materials from Gortyn.
The village's name dates back to 250 AD, when ten Cretan men were martyred here during the religious persecutions under the Roman Emperor Decius. The village was given the name "Ten Saints" in honor of these courageous Christian martyrs. The 12th-century church dedicated to "Agioi Deka" had a predecessor from the 5th century.