Choudhury was nominated by Bangladesh Nationalist Party to contest the 2018 mayoral election in Sylhet. He protested outside the office of deputy commissioner of Sylhet Metropolitan Police over the arrest of Bangladesh Nationalist Party activists who were campaigning on his re-election. He was re-elected mayor of Sylhet on 12 August 2018. He beat the Awami League candidate Badar Uddin Ahmed Kamran by 6,196 votes. He had also faced a rebel candidate, Badruzzaman Selim, of Bangladesh Nationalist Party and another candidate, Ehsanul Mahbub Jubayer, from Bangladesh Jamaat-e-Islami. Foyzul Haque Raju, an activist of Bangladesh Jatiotabadi Chatra Dal, died in fractional clashes near Choudhury's home after celebrating his election victory that day. He was sworn in on 5 September 2018 by Prime Minister Sheikh Hasina.
