The first portion of the line between Utica Avenue and Junius Street opened on November 22, 1920, with shuttle trains operating over this route.

In 1913, New York City, the Brooklyn Rapid Transit Company, and the Interborough Rapid Transit Company (IRT) reached an agreement, known as the Dual Contracts, to drastically expand subway service across New York City.

[10]: 192–193  On April 16, 1916, the New York State Public Service Commission (PSC) denied a request by the Chief Engineer of the IRT for the installation of a third track on the line to provide necessary space for train storage.

[11] On May 9, 1916, title was acquired to sixteen parcels of land between the intersection of Eastern Parkway and Buffalo Street and East New York Avenue opposite of East 98th Street in condemnation proceedings to complete the line.

[13] On June 5, the PSC accepted bids for 52,756 tons of structural steel to be used on multiple subway extensions to be completed as part of the Dual Contracts,[10]: 109–110  of which 15,100 tons of the steel were for the Livonia Avenue extension.

[17] Construction on the line began in spring 1917, and a quarter of the work that needed to be done before the erection of the steel was completed by September 1917.

In February 1920, a contract for the unfinished portion of the line was awarded to George W. McNulty and the Holbrook, Cabot and Rollins Company.

[22] During 1919, the city purchased an area of land bounded by Hegeman and Lawrence Avenues, and Elton and Linwood Streets for the construction of a storage yard.

[24] The first portion of the line between Utica Avenue and Junius Street opened on November 22, 1920, with shuttle trains operating over this route.

[27] The New Lots Line opened one more stop farther to the east to Pennsylvania Avenue on December 24, 1920.

[28]: 129–130  On March 15, 1921, a contract for the completion of a signal tower to control train movements at the terminal crossovers at New Lots Avenue, and at the entrances to Livonia Yard, was submitted to the New York City Board of Estimate.

[29][30] On May 18, 1922, work began on the installation of tracks in Livonia Yard,[24] and on June 9, 1922, the signal tower contract was approved.

[31] The approach tracks needed for the operation of through service to New Lots Avenue were completed on July 18, 1922.

[38] In 1961, work to extend the platforms at stations along the line to accommodate ten-car trains was completed.

[39] As part of an 18-month capital budget that took effect on January 1, 1963, the New Lots Avenue station was reconstructed.

[40] In 1968, as part of the proposed Program for Action, the IRT New Lots Line in East New York, would be extended southerly through the Livonia Yard to Flatlands Avenue to a modern terminal at Flatlands Avenue and Linwood Street.

This two-track line would have run at ground level and it would have provided better access to the then-growing community of Spring Creek.

[42][43] As of 2022[update], a potential extension of the IRT New Lots Line through Livonia Yard is being evaluated as part of the 2025–2044 20-Year Needs Assessment.

In 1975, the New York City Transit Authority (NYCTA) applied for a Mass Transportation Facilities Grant Application from the United States Department of Transportation (USDOT) to fund four improvement projects, including the replacement of wooden platforms with concrete platforms at Rockaway Avenue, Junius Street, Pennsylvania Avenue, and Van Siclen Avenue.

[48] The grant request was approved by the USDOT, and NYCTA invited contractors to bid on the platform replacement project in November 1976.

[49] From 2000 to August 2001, 3 train service was split into two sections to allow for the line to be rebuilt, with transfers available at Utica Avenue.

As part of the Metropolitan Transportation Authority (MTA)'s 2010–2014 Capital Program, funding was provided for a 25-station Station Renewal program, which focused on renovating stations with a high concentration of components rated 3.5 or worse on a five-point scale, with 5 being the highest.

As part of the project, station drainage, doors, windows, railings, platform rubbing boards, structural steel, panels and signage were replaced.

[55] In the third phase, Junius Street and Sutter Avenue–Rutland Road stations were closed for renovations from October 5, 2016, to June 19, 2017.

Passengers can transfer between the two stations for free by using an overpass running parallel to the New Lots Line, which allows pedestrians on Livonia Avenue to cross over the Long Island Rail Road's open-cut Bay Ridge Branch, and using a MetroCard or OMNY.

At the request of Brooklyn Borough President Eric Adams, and due to increasing ridership and plans for additional housing in the area, funding was provided to build the free transfer.

In addition, both stations would also have been upgraded to become compliant with mobility accessibility guidelines under the Americans with Disabilities Act of 1990.

[61] A free MetroCard-only transfer between the two stations was provided during weekends and late nights as part of the reconstruction of the 14th Street Tunnel starting in April 2019.