Born in Kolkata, West Bengal, Mukherjee started his football career with Army Public School, Calcutta.
[1] Mukherjee spent a year and a half with East Bengal before signing with Calcutta Premier Division side Aryan.
[1] On 9 August 2018, it was announced that Mukherjee, along with seven other Bengali players, had signed with Indian Super League side ATK.
[5] 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.