A good place to get this is the level mentioned in the guide for:
There are three guys at the beginning, a couple of which have pistols. Obtain a pistol from one of them, preferably by stunning them so you can headshot them, giving you an extra headshot. Now, headshot the guy around the next turn and the guys in the next room. If you run out of ammo, you can go back and pick up another pistol, as a total of two are available from the three guys at the start. The pistols are accurate and easy to use. You can also use shotguns and rifles for the headshots. Continue killing the guys in the next room, and the additional attackers who spawn after you kill them all. Pick up the whatever weapons they drop if you run out of ammo. Using this method, you can net several headshots per run. Continue until you reach 100 headshots to unlock this achievement. If you're going for this after you complete the Superhot.exe story, while trying to score some headshots, you'll already have obtained significant progress towards this achievement.