Serving as a portal for immigrants who wanted to start their new life in the United States, the Ellis Island was chosen as the site for the first Federal immigration station by the former president Benjamin Harrison in 1890. However, in the 35 years prior to the creation of the first federal immigration office, more than eight million migrants arriving at New York Harbor had been administered by New York State officials at Castle Garden Immigration Depot in lower Manhattan, just beyond the bay. From 1892 to 1954, more than twelve million settlers were processed in the first immigration station where they will only have to wait for several hours to be granted entry to the country.

The Ellis Island was originally 3.3 acres in size when it was acquired by Samuel Ellis (thus the name Ellis Island) and attempted to sell it in 1785, but was unsuccessful. Over the years, its size expanded to 27.5 acres, mostly by landfill obtained from ship ballast and possibly excess earth from the construction of the New York City subway system. The original and natural 3.3 acres portion of the island is part of New York while the rest is part of New Jersey.

Before Samuel Ellis acquired the island, Ellis Island had been known by various names. Local Indian tribes called it "Kioshk" or Gull Island. During the Dutch and English colonial eras, the island was known for many generations as Oyster Island because of its rich and abundant oyster banks and profitable shad runs. It had also been called Dyre, Bucking and Anderson's Island.

In 1794, the state of New York leased the island but due to the questionable ownership of the landmass, the United States government, through a legislation passed in 1807, seized the island that was used as a federal armory from 1808 to 1814. For 80 years from the end of the War of 1812, the island was home to Fort Gibson and continued to be used as a military post.

To accommodate the growing number of immigrants to the United States, a three-story tall wooden immigration station was built on the New York section of the island. This time, the state of New York is no longer in charge of the immigration management but the federal government which assumed control on April 18, 1890. When the first federal immigration post opened on January 1, 1892, three large ships disembarked here and 700 immigrants passed over its docks. In its first year, almost 450,000 migrant applicants were processed at the station.

Sadly, a fire on June 15, 1897, destroyed the entire structure and turned it into ashes. Though no losses of life were reported, records of about 1.5 million immigrants that have been processed in the station in its five years of operation and those dating back to 1855 were devastated. A replacement was immediately constructed and a French Renaissance Revival style structure made of red brick with limestone trim opened on December 17, 1900.

Its use as an immigration processing post was ended after the Immigration Act of 1924 was passed which greatly restricted immigration and Ellis Island became primarily a detention and deportation processing center.

The Ellis Island is now an immigration museum and is part of the Statue of Liberty National Monument.