A witch-hunter is a someone who hunts witches, for purposes of trial and execution. They don't discriminate. They also hunt warlocks. If they're feeling really uppity, they might even go after a vampire or a werewolf, but this would make them vampire hunters and werewolf hunters (duh). Witch-hunters were mostly prominent in Europe during the 16th and 17th centuries. Some refer to this period as "Burning Times" as it relates to woman (usually innocent) who would be accused of witchcraft and subsequently executed.
On the CW Network television series The Secret Circle, there was a character named Isaac, who led a team of hunters to eradicate a coven of witches operating in Chance Harbor, Washington. Ironically, Isaac employed the services of a young magic user named Jake Armstrong to facilitate this goal.