The story begins in 1784, when Russians led by Grigorii Shelikhov massacred several hundred Alutiiq men, women, and children at "Refuge Rock," a small islet by Sitkalidik Island. The Russians held Alutiiq hostages at Three Saints Harbor before moving to their new headquarters at Pavlovski Gavan (Paul's Harbor, later called Kodiak) in 1793. The settlement they left behind at Three Saints now became known as the "old harbor." Its Alutiiq residents still had to work for the Russians by hunting sea otters and producing foods such as dried fish, whale meat, and berries. By the late 1800s, Old Harbor had been moved several times, finally ending up in its present location at the north end of Sitkalidik Strait on eastern Kodiak Island.

Old Harbor has been a refuge for people from many other villages, so that its families have widespread kinship ties. Survivors of the terrible smallpox epidemic of 1837-38 were sent to live there, and people from the old villages of Aiaktalik and Eagle Harbor resettled at Old Harbor during the 20th century. Old Harbor residents worked at canneries and at the whaling station at Port Hobron. Today many are commercial fishermen. The village was heavily damaged by tidal waves after the 1964 Great Alaska Earthquake, but the 19th century Orthodox church was spared and residents were able to rebuild their homes. The population of Old Harbor in 1990 was 284.