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.
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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.
There have been several deadly attacks in Bangladesh in recent months, although it is not clear who is behind them.
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.
There have also been attacks on members of religious minorities including Shia, Sufi and Ahmadi Muslims, Christians and Hindus.
Two foreigners, an Italian aid worker and a Japanese man, were also shot dead late last year, in seemingly random attacks.
The so-called Islamic State group has said it carried out many of the attacks - but this has not been independently verified.
Members of another militant Islamist group, the Jamaat-ul Mujahideen Bangladesh (JMB), were arrested over an assault on an Italian Catholic priest late last year.
A Bangladeshi law student who had expressed secular views online has been killed in the capital, Dhaka.