Born in Kolkata, West Bengal, Mukherjee started his football career with Army Public School, Calcutta.[1] In 2013, Mukherjee represented the school's football side in the Keventer Cup. He played the tournament at center back and impressed enough to earn a spot in the tournament's All Star side.[1] In 2014, during a friendly match against East Bengal U19, Mukherjee impressed East Bengal's coach and was selected to join the squad.[1]
Mukherjee spent a year and a half with East Bengal before signing with Calcutta Premier Division side Aryan.[1] After sporadic appearances in his first season, he got a regular starting role during his second year. Mukherjee's performances with Aryan earned him a selection into West Bengal's squad for the Santosh Trophy in 2017 and 2018.[1][2] His performances for West Bengal's winning squad in 2017 earned him a deal with Mohammedan. With Mohammedan, Mukherjee played for the club in the Calcutta Premier Division and I-League 2nd Division.[1]
ATK
On 9 August 2018, it was announced that Mukherjee, along with seven other Bengali players, had signed with Indian Super League side ATK.[3] He made his professional debut for the club on 10 November 2018 against Pune City. He came on as a 74th-minute substitute for Aiborlang Khongjee as ATK won 1–0.[4] Mukherjee then earned his first start during ATK's next game against Mumbai City on 24 November. The match ended in a 0–0 draw.[5]
East Bengal
On 2 January 2021, it was announced that Ankit has signed for Kolkata giants East Bengal with a free transfer from ATK Mohun Bagan.[6] On 3 January, he made his debut for East Bengal as he came on in as a substitute in the 73rd minute for Raju Gaikwad as the team won 3–1.[7]