Originally part of Burlington County, Little Egg Harbor took its name from the portion of a bay called Egg Harbor (known today as Little Egg Harbor) by the Dutch sailors because of the eggs found in nearby gull nests. The first known account of the town was made by Captain Cornelius Jacobsen May in 1614.

The first European to settle the township was Hendrick Jacobs Falkenberg, who likely arrived by 1693 when he does not appear on a census of the Swedes along the Delaware River, where he had lived for nearly three decades.[9] Though he was from Holstein (now in Germany), his first wife was a Finn and part of the Swedish community. Falkenberg settled on an 800-acre tract of land that he had acquired from the Lenni Lenape Indians in 1674, and a 1697 deed re-confirmed this earlier purchase. This tract included the two islands of Monhunk and Minnicunk later known as Wills Island and Osborn Island.

Falkenberg was a linguist, fluent in the Lenape language, and was considered southern New Jersey's foremost language interpreter involving land transactions between the Indians and the European settlers, particularly the English Quakers.

In October 1778, the Little Egg Harbor Massacre took place as Patrick Ferguson was wreaking havoc on Colonial shipping in the Mullica River. Kazimierz Pułaski and his newly raised forces were ordered to oppose his actions. Pulaski's Legion, along with three companies of light infantry, three troops of light horse, and one artillery detachment, came too late to be of great use against Ferguson's operations. But their arrival did stop Ferguson from raiding the iron works at Batsto, and stemmed their attacks on privateers at The Forks of the Mullica River.

They then set up camp on a farm. A deserter, Lt. Gustav Juliet, found Ferguson and told him of Pulaski's encampment; he mentioned that morale was fairly low, and security almost nonexistent, so that a surprise attack would be devastating. Ferguson promptly loaded 250 of his best men onto boats and rowed them, in the dark, some ten miles (16 km) to Osborne Island. He then marched them a further two miles (3 km) to the site of the infantry outpost, which comprised fifty men a short distance from the main encampment. At first light, Ferguson ordered the attack; only five of his quarry were taken alive. Pulaski eventually led his mounted troops up, causing Ferguson to retreat to his boats minus a few men that had fallen into the colonists' hands. A memorial on Radio Road commemorates the attack.

One of the first recorded ships of the township was a sloop belonging to Thomas Ridgway Sr. John Mathis Sr. also had a ship which his son, Daniel, sailed the West Indian routes. They made a profit from selling clams and oysters.

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