The attack comes within a day of the suicide bombing of RAB's temporary base at Ashkona, where the future headquarters of the elite force is to be constructed.
Khilgaon-based RAB-3 chief Tuhin Mohammad Masud told bdnews24.com: “A man on a motorcycle tried to intrude into the checkpost at Shekher Jaiga area around 4:30am prompting RAB personnel to open fire."
The elite police unit said two of its men have been injured in Saturday's attack.
RAB initially reported the attacker was seriously injured, but senior officer Tuhin later confirmed his death.
Around 11am, RAB's bomb experts arrived on the spot to defuse the explosives found on the suspected attacker.
The identity of the man and the group he possibly belonged to were not yet known.
After the raids on militant hideouts at Chittagong's Sitakunda, a suicide bomber blew himself up on Friday at the RAB barracks in the capital's Ashkona, injuring two RAB personnel.
Intelligence officials said the two successive attacks were worrying because it pointed to the 'continued existence' of a terrorist command structure directing the suicide attacks.
Amid security forces' crackdown on militancy following the Gulshan and Sholakia terror attacks in July last year, the militants had appeared weakened, but recent incidents suggested that they were re-grouping and a leadership was in charge.
On Mar 6, a prison van carrying death-row convict Harkat-ul-Jihad-al-Islami (HuJI) leader Mufti Hannan from court to Gazipur's Kashimpur prison came under a bomb attack, in what the police say was an attempt to snatch the militant leader.
The next day, two suspected members of Neo-JMB were nabbed after they hurled bombs on policemen at a highway checkpost in Comilla.
The same night, police's counterterrorism unit took one of them to Chittagong's Mirsharai and busted a hideout. A large amount of bombs and explosives were recovered from a house at the Upazila town.
Police raided another house in adjacent Premtala area the same day on information given by the couple.
The second raid ended 19 hours later through an assault which saw the deaths of two militant suspects in a suicide blast and two others shot dead. A child also died in the explosion.
But for Friday's Ashkona RAB barracks attack, its mouthpiece only reported the incident without claiming any links to it, according to SITE Intelligence, a jihadist monitoring group.
Bangladesh law enforcers have, however, continued to maintain that there is no existence of IS in the country.