It ran from West Wareham on the Cape Cod main line of the Old Colony Railroad, southwest to Fairhaven, a town across the Acushnet River from New Bedford.

After graduating from high school in 1857, "Hen" Rogers hired on with the Fairhaven Branch Railroad as an expressman and brakeman.

Eventually, Henry Rogers rose within the growing petroleum industry to become one of the three key men in John D. Rockefeller's Standard Oil trust.

Beginning in the 1920s, automobiles and improved highways began to provide major competition to the New Haven.

The railroad tried a couple of times in the 1940s to end service and abandon the Fairhaven Branch, but vocal shippers protested.

In 1969, the Penn Central Railroad, created out of a merger between the New Haven, New York Central and Pennsylvania Railroads, took over operations of the New Haven and hauled the loads of sand the 2.5 miles between the sand pit and Tremont Junction, where they would be picked up by the Cape Cod local freight.

On March 7, 1992, a passenger excursion run by the Cape Cod Railroad ran down a short portion of the overgrown and dilapidated Fairhaven Branch.

[1] In 1996, a local resident built a narrow wooden bridge across the outlet channel of Eel Pond in Mattapoisett, enabling use of a 0.5-mile (0.80 km) section of the former right-of-way for recreation.

[1] That year, Old Colony Regional Vocational Technical High School students rebuilt the bridge over the Mattapoisett River, allowing use of a further 0.4 miles (0.64 km) of unpaved right-of-way.

[5][6] In February 2019, MassDOT awarded a $7 million contract for the construction, with notice to proceed given in late March.

[11] Mattapoisett plans to complete an additional 0.5-mile (0.80 km) connecting segment to reach Industrial Drive from the Marion line; the state awarded $110,000 in construction funds in July 2020.

[12] As of November 2020[update], the 1.5-mile (2.4 km) section along Industrial Drive was expected to begin construction in spring 2021.

Today, the location of the station and the yard at Railroad wharf is occupied by The Woods Hole, Martha's Vineyard and Nantucket Steamship Authority maintenance facility.

From here passengers would disembark and await a train to Boston, or Cape Cod, depending on their destination.

Several other smaller customers utilized the line to ship their goods, including a coal dealer in Mattapoisett, and a sand pit in Marion, owned by the Whitehead Brothers Company of New Jersey.