Port Allen Harbor is located on the southern shores of Hawaii's Kauai island, the northernmost island in the Hawaiian chain. It is about 18 nautical miles (25 kilometers or 15 miles by air) west-southwest of Nawiliwili Harbor on Kauai's southeastern coast. It is also about 106 nautical miles (165 kilometers or 103 miles by air) from Honolulu Harbor on Oahu.

Located on the shores of Hanapepe Bay, Port Allen Harbor is near the cities of Eleele, with a population of about two thousand, and Hanapepe, home to over 2100 people. Historically known as Eleele Landing, Port Allen Harbor is now the island's second harbor.

In late 1840, Charles Wilkes led the United States Exploring Expedition in visiting Hanapepe Bay and the future Port Allen Harbor. Hanapepe is one of a handful of towns in Hawaii that was not created by the establishment of sugar plantations.

Port Allen Harbor got its modern name in the early 1900s when the Kauai Railway, a narrow gauge railroad, connected Eleele Landing with Koloa and Kalaheo on Kauai's south coast. At that time, the Railway changed the name to Port Allen Harbor in honor of Samuel Cresson Allen. Allen had provided much of the funding to improve and expand Port Allen Harbor.

In 1924, the Hanapepe Massacre (also known as the Battle of Hanapepe) ended with 20 fatalities when local police and Filipino sugar workers clashed.

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