After emerging from the tunnel under Fourth Avenue, the two separate Sea Beach tracks rise on either side of a ramp which formerly connected to the original line to the Brooklyn shore at 65th Street in Bay Ridge.

The express tracks end south of 86th Street as the line becomes double-tracked, and cut diagonally adjacent to the Coney Island Yards.

Only the northbound (E4) track was rehabilitated, however, for two-way traffic from its northern end to Kings Highway if needed.

On the Coney Island end, the original path curved left soon after the curve to the right at the northern edge of the Coney Island Yards, ending at the combined Sea Beach Palace hotel and depot, on the north side of the BMT Brighton Line at around West 10th Street.

A March 1, 1907, agreement allowed the company to operate through service from 38th Street and New Utrecht Avenue to Coney Island.

Starting around 1908, electric trains began operating as a branch of the BMT West End Line from Bath Junction to Coney Island, with trains coming from Park Row in Manhattan via the Brooklyn Bridge and BMT Fifth Avenue Line.

[10] The tracks over the north side of the Manhattan Bridge opened on September 4, 1917, along with part of the BMT Broadway Line.

The NX began on November 27, 1967, as a "super-express" from Brighton Beach on the BMT Brighton Line through Coney Island–Stillwell Avenue, and along the Sea Beach Line express tracks to 57th Street with only seven stops between Stillwell Avenue and 57th Street, three in Brooklyn and four in Manhattan.

This service was discontinued on April 15, 1968, due to low ridership, and no regular trains have used the Sea Beach express tracks since.

In the 1970s, there was a proposal to renovate the Sea Beach open cut, which was deteriorating to the point that a retaining wall along the line was in danger of collapsing onto the tracks.

[16] More than $20 million was earmarked for New York City Subway projects in 1977, including for upgrades to the Sea Beach line.

[17] In 1986, the New York City Transit Authority launched a study to determine whether to close 79 stations on 11 routes, including the entire Sea Beach Line, due to low ridership and high repair costs.

[18][19] Numerous figures, including New York City Council member Carol Greitzer, criticized the plans.

At Bay Parkway and Eighth Avenue, temporary wooden platforms were placed on the southbound express trackbed.

[28][29] The southbound platforms at Kings Highway, Avenue U, and 86th Street reopened on October 29, 2018, with closures lasting a month less than for their northbound counterparts.

From October 21, 2019, until April 27, 2020, N trains terminated at 86th Street so work could be completed to protect Coney Island Yard from flooding.