Lets say the magnetron indeed has a power requirement of 1kW (I never tried, so I might be off with this value and 1kW is not enough to burn a brain. On the other hand, I guess it also depends on the duration the magnetron is turned on.)
Lets also say a mobile(-ish) battery of 50V is used (I do have to pick some value, right).
P = V * I , so it would draw 1000W / 50V = 20A.
Now, lets say a brain is fried in 1 minute (maybe this assumption is too high: if it takes too long the 'immediate dying' effect would be gone? Although some agony is a pro in the eyes of an evil mastermind)
So this battery for example (disclaimer: first one I found; I do not own stock for this company) seems to be sufficient. As it should be able to power it for about 1 hour (19.5Ah)... It is a bit heavy with its 8.8kg, but we do probably not need power for one hours, so a smaller battery should be sufficient, weighing a lot less.
So in short the answer is (with these crude estimates and calculations): Yes it is possible to power a (mobile-ish, the magnetron you linked to did not look too mobile as well) device with our current technology.
I did not read the manga or anime, but I guess the complete system needs to be scaled down to match the description and fit in a helmet...