In 1997, Robert Kraft, the owner of the National Football League's New England Patriots, and Massport, a state government agency that runs airports and sea ports, tried unsuccessfully to build on the lot the South Boston Sports Megaplex, which included a new home stadium for the football team to replace Foxboro Stadium.

Chapter 152 authorized the acquisition by eminent domain of approximately 60 acres (0.24 km2) of land in the Seaport area of Boston.

The new convention center was designed by Rafael Viñoly Architects, New York City, in association with The HNTB Companies, Boston.

[10] The New England Auto Show, long a staple for the Bayside Expo Center in the Dorchester section of Boston, moved to the new BCEC and signed on through 2009.

[14] In the 2010s, a new Indigo Line was proposed by Governor Deval Patrick, using diesel multiple units (DMUs), to connect the BCEC to Back Bay Station and the many hotels there.

Funding for DMUs was cut by Governor Charlie Baker, and Track 61 was instead converted to test newly manufactured trains for the MBTA Red Line.

In April 2020, the Convention center was set up as a 1,000 bed alternate care site for COVID-19 patients as part of the government response to the COVID-19 pandemic in Boston, which had also eliminated demand for conferences.