Faisal Arefin Dipon, 43, was killed at his office in the city centre, 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 Mr Roy.
Mr Dipon was found dead at the Jagriti Prokashoni publishing house, in his third-floor office.
"I saw him lying upside down and in a massive pool of blood. They slaughtered his neck. He is dead," his father, the writer Abul Kashem Fazlul Haq, said, quoted by AFP.
Earlier on Saturday, armed men burst into the offices of publisher Ahmedur Rashid Tutul.