The sect also threatened to deal with the Chief of Army Staff, Lt. Gen. Tukur Buratai.
The video was published by NE on Wednesday.
It showed a large number of members of the terrorist group observing what they claimed was their Eid-el-Kabir prayer at an undisclosed location.
The unnamed leader of the group who led the prayers was dressed in a white-flowing gown and black turban. He held an AK 47 rifle.
He addressed the crowd in the Arabic and Hausa languages.
The speaker declared the sect’s continued allegiance to Shekau after which he vowed on behalf of other members to continue to unleash terror on Nigerians.
In a direct message to President Buhari, the sect’s leader who did not give his name said, “This is a message to the leader of the infidels (President Muhammadu) Buhari, who says he will crush us. Infidels before him made similar threats, Buhari who says he will crush us; in sha Allah (by the grace of Allah) he will only die.
“By the grace of Allah, under the leadership of the leader of this movement our Imam (Shekau), we will capture Buhari hand to hand.
“This message we are sending out today is not an old one. We prepared it today, Monday, 12 September, 2016 in the calendar of infidels. (Lt. Gen. Tukur) Buratai, we will deal with all our enemies, we are prepared at all times. Just as you all love life, so do we love death.
“This time around, no retreat, no surrender, in sha Allah. We shall be granted victory over you all.”
Reacting to the new threat against the President and the Army Chief, the Defence Headquarters urged Nigerians to ignore the sect.
The Acting Director Defence Information, Brig. Gen. Rabe Abubakar, described the threat as empty, lacking in substance and a joke.
Abubakar said the military had dealt with the insurgents in such a way that they had migrated to the cyberspace to make empty threats.
He said the latest video by the insurgents was an attempt to remind Nigerians that they once existed.
He stressed that the military was aware of what it had done and was still planning to do to the insurgent group.
Abubakar, who described the video as a sign of weakness, said the threat posed by the group was almost being brought to an end.
He said, “We don’t have any comment. We know what we have done, and what we are planning to do. The only place they have agenda for now is the social media.
“The only ground the Boko Haram can go to hide and pretend to be alive is the social media because it is everybody’s home.
“The so-called video is an attempt by the remnants to remind us that there were once some Boko Haram elements.
“The issue of the threat to capture PMB is a complete joke and a dream of the century. Therefore, the entire clip should be ignored as everybody is appreciative of our feat against Boko Haram.
“It is not just an empty threat; it is a threat that has no substance at all. It is a senseless threat from their imagination. Nigeria should simply ignore it.”