It was built for $161 million at Avondale Shipyard in Louisiana, along the Mississippi River near New Orleans,[4] and brought to New York in 1992 to reduce overcrowding in the island's land-bound buildings for a lower price.

[8] The idea of temporarily alleviating the issues of a growing inmate population and dwindling space by outfitting jail ships was conceived under the administration of then Mayor Edward I. Koch.

[4] At the time, the jails at nearby Rikers Island held 22,000 inmates, and with this number increasing consistently, were nearing capacity.

Due to unanticipated construction problems including issues with the ventilation system, the finished barge was delivered 18 months late and $35 million over budget.

[9] On January 26, 1992, the recently outfitted jail barge was brought through Long Island Sound by the tugboat, Michael Turecamo, after an 1,800 nautical mile trip.

[4] By the time the Bain Center opened, the inmate population of New York City's jail system had started to decline.

[22] The six-month campaign expected more than seven thousand additional arrests than usual, but the ship was not reopened until 1998 when it was used by the Department of Juvenile Justice.

[23] In early 2016, New York City government officials began looking into ways to possibly shutter Rikers Island and transfer prisoners to other locations.

[25] In 2018 the city released plans to phase out Rikers Island over ten years[26] and replace it with borough-based jails.

[27] The Bain Center was included in the plan to close Rikers Island,[9] which the New York City Council voted to approve in October 2019.

Opponents of the barge's continued operation said the facility's inmates, who were largely Hispanic and black, were incarcerated "with minimal oversight".

[30] In September 2023, the city's Department of Corrections announced plans to decommission the Vernon C. Bain Center by that October.

[30] The jail barge was located in Hunts Point in the South Bronx, about 5 miles (8.0 km) from SUNY Maritime College at Throggs Neck.

[9] By the 2020s, detainees were grouped into extremely small, poorly lit dormitories that were rusting, and the barge sometimes leaked during rainstorms.

[44] Prior to 2002, an inmate tried to escape from the jail's recreation area by climbing the 30-foot fence equipped with razor wire.

[46] The corrections commissioner said the escape was caused by a combination of the inmate's quick thinking and the officers' sloppy work.

[47] In early 2013, an inmate charged with petty larceny successfully slipped out of his handcuffs as he arrived at the Bain Center.