Apart from the I-League 2 (formerly), the reserve side plays in the Calcutta Football League, currently under the sponsorship name Emami East Bengal Club.

The East Bengal Academy was re-instated on 20 June 2016 with the motive to establish a strong footprint in Indian football by producing quality professional players.

[2] The East Bengal Academy was founded in the early part of the 21st century and had a major success initially as the U-19 East Bengal team won the first two U-19 National Football leagues held in 2001-02 and 2002-03[3] and then the club's Under-15 team qualified for the Manchester United Premier Cup after being champions of India defeating Mahindra United 1–0 in the final,[4] and becoming South–East Asian regional runners up in 2007.

In 2018, the East Bengal Reserves team coached by Ranjan Chowdhury won the Darjeeling Gold Cup, defeating another Kolkata giant Mohammedan Sporting in the final.

[16] The club also bolstered the squad by making some top signings from the Santosh Trophy teams, including five players from Kerala, the champions of the 2021–22 edition.

[32] East Bengal U-21 qualified for the 2024 Next Gen Cup to be held in Birmingham, United Kingdom along with Punjab and Muthoot FA from India.

[37] The National Football League U-19 was launched in 2001 and the East Bengal U-19 team won the inaugural edition defeating India sub-juniors 3–2 in the final.

[39] The team also finished runners-up in the 2003–04 edition as they lost to their rivals Mohun Bagan U-19 3–1 in the penalty shoot-out after the final ended 0–0 in regulation time.

[3] After the tournament was restarted as the I-League U19 in 2008 and later renamed to Elite League, the East Bengal team became runners-up four times, failing to win to the title.

[41] The East Bengal Under-17 squad for 2023-24 season[42] Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.

[58] The East Bengal Academy Under-15 squad for 2019–20 season Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.

[67] The East Bengal Under–13 squad for the 2023–24 season Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.