Nazimuddin Samad was hacked with machetes at a traffic junction late on Wednesday and then shot, police said.
The 28-year-old was reported to have been an organiser of the Ganajagran Manch, a secular campaigning group.
A string of prominent secular bloggers have been attacked or killed by religious extremists in Bangladesh in the last year.
Bangladesh is officially secular but critics say the government has failed to properly address the attacks.
‘I have no religion’
Police said three assailants on a motorcycle attacked Mr Samad and then shot him, The Dhaka Tribune reported.
Police have not named any suspects in the case nor confirmed a religious motive.
Mr Samad, a student of Jagannath University, regularly wrote against religious extremism on his Facebook page. He had written “I have no religion” on his profile under religious views.
Last year, four prominent secular bloggers were killed with machetes, one inside his own home.
They all appeared on a list of 84 “atheist bloggers” drawn up by Islamic groups in 2013 and widely circulated.