The original wooden station was replaced by a larger structure in 1848, and the Saugus Branch began serving Lynn in 1855.

In the "Great Lynn Depot War", a local disagreement in 1865 about where to place a replacement station became a major court case.

The Boston and Maine Railroad (B&M), which had acquired the Eastern in 1883, began a grade separation project through Lynn in 1909 – part of an attempt to quadruple-track the whole line.

The MBTA opened a new accessible island platform in 1992, along with a large parking garage that anticipated a never-realized extension of the Blue Line.

The rail station and parking garage temporarily closed on October 1, 2022, pending a reconstruction project, while the busway remained open.

[5]: 28 On June 16, 1846, the stockholders authorized the sale of $450,000 of new stock to fund various branch lines plus new depots at Salem and Lynn.

[5] In 1845 and 1846, a line from Malden to Salem via Saugus and Lynnfield was proposed but did not pass the legislature due to bitter objections from the Eastern.

[5] Lynn became the primary turnback point for the Saugus Branch after 1855, though a limited number of trains continued to Salem until World War I.

[9] On November 19, 1888, the Highland Circuit route of the Lynn & Boston became the first electrified trolley line in Massachusetts.

[12] The Central Square faction was aided by a bill passed in the Massachusetts legislature on April 29, 1865, which disallowed a railroad from abandoning a station that had been in service more than five years, as well as an 1868 bill that specifically directed the Eastern Railroad to build the replacement station at Central Square.

The Market Street station was demolished in 1873 and replaced with a wooden shelter that served only a handful of trains.

[13] The depot controversy was a setback for the Eastern Railroad in a city where residents were already dissatisfied with poor service.

In 1872, the Boston, Revere Beach and Lynn Railroad (BRB&L) was charted as a direct competitor to the Eastern; service began from Market Street in 1875 and lasted until 1940.

[4] The 1872-built Central Square station was severely damaged in the Great Lynn Fire on November 26, 1889, which burned much of the downtown area.

[19] As early as 1901, the city began planning to eliminate the numerous grade crossings in downtown Lynn.

With 150 trains per day on the main line and 40 on the Saugus Branch, some streets were blocked for as long as half of daylight hours.

Vernon and Exchange streets, was in the same flat-roofed brick style as Winchester Center and Wedgemere built five years later.

[23] By the late 1977, the station was a "shambles", with "broken glass, garbage, vulgar graffiti and crumbling cement.

[25] A $41.3 million construction contract for the station and garage was awarded on April 13, 1988, with completion expected in fall 1989.

[27] Along with the pair at Framingham, the remaining elevator was one of the few on the commuter rail system maintained by the MBTA, rather than by Amtrak or local agencies.

[28] In 2003, the MBTA spent slightly less than $100,000 to rehabilitate the deteriorated garage and to convert the drop-off lane into a full busway with shelters, benches, and signage.

In September 2008, the MBTA board authorized a $1 million tie replacement and slope stabilization project at the station.

[34] Lynn and River Works stations were changed from fare Zone 2 to Zone 1A (allowing subway-fare rides to Boston) from May 22–31, 2020, and July 1, 2020 – June 30, 2021 to provide additional travel options during the COVID-19 pandemic (as many of the 400-series bus routes were reduced in frequency) and to examine the impact of temporary fare changes.

[35][36] The change was found to have diverted just 8 daily riders to commuter rail, and the stations reverted to Zone 2 on July 1, 2021.

[37] The MBTA began planning a major station renovation in 2019; a $3.1 million design contract was awarded in 2021.

[42] Construction of the temporary platforms, which reused concrete slabs used by the Big Dig, began in August 2023.

[51] As of June 2023[update], the new permanent station is not expected to be complete until 2030, a timeline that was criticized by local officials.

Despite numerous studies on the project and previous bond bills, there is currently no identified funding source; due to the MBTA's constrained finances, construction is not likely to begin soon.

The 1992-built Lynn parking garage, designed for the capacity needed for the Blue Line extension, does not fill fully from commuter rail ridership.

Besides its downtown stops, the Eastern Railroad also served East Lynn from 1880 until Marblehead Branch service ended on June 14, 1959.