The concept was proposed in March 1954 and backed by a $658 million construction program. In 1963 the idea to add an LIRR track to the GCT-Queens connection was proposed, and construction began in 1969.

The MTA was only able to complete about 2/3rds of the tunnel before the financial crisis of 1975 put an end to ESA.

In 1997 Senator Al D'Amato asked for federal funds to complete the project. In 1999 the MTA proposed $17 Billion to capital projects with $1.6 Billion going to East Side Access. The idea was that it would complete within 10 years.

The rejuvenated project flew through red tape relatively quickly, with the final plan approved in 2002 and the land acquired in 2003. After finally getting funds approved and choosing their contractor in 2006, construction resumed in 2007 once the new boring machines arrived.

From 2007 till now, ESA was under construction. Total time from first being proposed to the public until opening was 69 years and 10 months. Time from first shovel dig to opening was 53 years and 4 months. Time from the its 2007 restart until opening was 15 years and 4 months.