Faisal Arefin Dipon, 43, was killed at his office in the city center, hours after another publisher and two secular writers were injured in an attack.
They are the latest victims in a series of deadly attacks on secularists since blogger Avijit Roy was hacked to death by suspected Islamists in February.
Both publishers published Avijit Roy.
Faisal Arefin Dipon was found dead at the Jagriti Prokashoni publishing house, in his third-floor office.
Earlier on Saturday, armed men burst into the offices of publisher Ahmedur Rashid Tutul.
They stabbed Ahmedur Rashid Tutul and two writers who were with him, locked them in an office and fled the scene, police said.
The three men were rushed to hospital, and at least one of them is in a critical condition.
Avijit Roy, a US citizen of Bangladeshi origin and critic of radical Islamism, was murdered in February. His wife and fellow blogger Bonya Ahmed was badly injured in the attack.
Three other Bangladeshi bloggers have since been killed.
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