The shuttle service uses the BMT Franklin Avenue Line exclusively and operates 24 hours a day.

A major blow to through service viability occurred in 1954 when the D train of the IND Division was extended to Coney Island via the Culver Line, depriving the Franklin of a major source of transfer traffic, consisting of passengers from Harlem and the Bronx, who now had a more direct route to Coney Island.

[10][11] Brighton–Franklin Sunday express service ended after the 1956 summer season, though it continued for several years as a summer-only local.

The last through service, on Saturdays, ran on February 16, 1963 in advance of new BMT schedules in effect the next day,[12] resulting in the 7 Franklin Avenue Line becoming a full-time shuttle.

[13][14][15] On December 1, 1974, a southbound shuttle train of R32s was approaching the tunnel portal en route from Franklin Avenue when it derailed on the crossover at Empire Boulevard and smashed into the same place where BRT car 100 had hit in the Malbone Street Wreck.

This derailment resulted in some injuries, with R32 car 3668 damaged beyond repair, but there were no fatalities, because time signals limit the speed of trains coming down the hill from Crown Heights.

At the time, only 10,000 passengers used the shuttle per day, and in addition, the Franklin Avenue Line was severely deteriorated.

It was shrunk in size to only two cars, and the Dean Street station, which only had 50 paying riders per day, was closed in 1995 due to extensive fare evasion.

They argued that subway station repair work occurred elsewhere, while no attention was paid to the Franklin Avenue Shuttle.

[20] In the end they convinced the New York State Assembly to force the MTA to rebuild rather than abandon the line, and as a result most of the supporting infrastructure and stations were completely rehabilitated for 18 months, between July 1998 and October 1999 at a cost of $74 million.

[9][21][23] As of 2008[update], the Franklin Avenue Shuttle is the most punctual train in the New York City Subway system with a 99.7 percent on-time average.