Rapidly Destroy the Thalamus
Simply destroying the brainstem is not enough. Experiments during the Reign of Terror with guillotine victims shows that a decapitated person can remain conscious for up to 30 seconds, even capable of responding to their name being called out.
You need a way to effectively end consciousness as rapidly and immediately as possible. Enter the thalamus.
The thalamus has often been referred to as the "hub" or "switchboard" of the brain. All of your senses save smell must pass through the thalamus before being interpreted by the higher cortex. The thalamus is also associated with regulating wakefulness and consciousness.
But neurologists have a suspicion that the thalamus is much more than a simple hub. It is very likely that the thalamus is, itself, the part of the brain that is "conscious" in the sense that it is the part of the brain that experiences qualia.
EEGs have shown that when the thalamus is inactive, the cerebral cortex enters a "standby" state, waiting for input from the thalamus. This is seen in experiments that selectively shut down the thalamus and in comatose stroke victims whose cortex is intact, but whose thalamus is not.
In addition, the experience of users of the drug ketamine lends credence to the "thalamus is the part of the brain that is conscious" view, specifically the experience of a "k-hole," in which users describe the bizarre and paradoxical sensation of being conscious of "nothing."
In it, they can hear nothing, see nothing, feel nothing, remember nothing, think nothing, but yet are somehow still aware they exist.
EEGs from experiments in sheep have shown that the k-hole state is one in which the cortex is shut down, but the thalamus is quite active.
Similarly, there is the fact that even brain damage which destroys large portions of the cortex does not result in coma, but a relatively small amount of damage to the thalamus does.
This leads to the very intriguing idea that the cortex, despite being the newest and most advanced part of the mammalian brain, is not itself "conscious," and instead merely processes information for the thalamus, which is the part of the brain that actually "experiences" the sensations. In this theory, the thalamus receives input from the senses, sends it to the cortex, which then interprets the data and sends it back to the thalamus as sensations. It is these "thalamo-cortical loops" that are the basis of the human mind.
So long story short, if you want to rapidly end consciousness, the best way to do that is to rapidly end the part of the brain experiencing the consciousness.
Unfortunately, that is easier said than done. The thalamus is at the direct center of the brain, about as deep into the skull as you can get.
There are a number of ways you could do it. The most obvious is the rapid pneumatic rod that others have mentioned. You just have to ensure that it hits directly into the thalamus.
Another, shall we say "less invasive," method would be to use microwaves, or perhaps even high energy gamma rays, to destroy the tissue in the thalamus.
There is a procedure for non-invasive operation on brain tumors called the Gamma knife. In it, multiple very narrow gamma ray beams are made to intersect on a specific point inside the brain (presumably the tumor). Any single gamma ray itself does not carry enough energy to harm the tissue, but the point where the beams overlap experiences a tremendous amount of ionizing radiation.
In theory, you could do the same thing with RF or microwaves, but given gamma rays have much more energy and a much shorter wavelength, they can be formed into a much smaller knife, allowing for fine, delicate ablation to very small areas, which will spare surrounding healthy tissue.
However, in your case, that doesn't matter, since the point of the exercise is to end the patient, so you could build a device much cheaper and simpler using RF and/or microwaves.
The overlapping microwaves could be triangulated on the thalamus, and as they heat it up, the cells would rapidly die, leading to loss of consciousness.
Rather disturbingly, it appears this technology already exists in our world and has been used against humans. A few years ago, after the US reopened relations with Cuba, many US diplomats were suddenly stricken with traumatic brain injury after being exposed to some kind of device in their rooms.
An investigation showed that they were most likely the victims of some kind of attack with a device that exposed them to high energy microwaves. The microwaves caused heating of their brains, which in turn lead to the damage.