Witchcraft has probably been around as long as humanity has in some form or other. It can take many forms, from a shamanic and animistic practice to one that uses very formal and complex rites, rituals and correspondences. At the heart of witchcraft, is the ability to create change in the world, to take control of aspects of life and the natural world in order to bring about the desired outcome.
It is difficult to separate witchcraft from religious or spiritual traditions found in the history of ancient humanity. As we simply do not know what they believed, we can only make assumptions based on what we find through archaeology and anthropology. There are tantalising examples of cave art from our Stone Age ancestors, where we see human beings with animal qualities performing rituals of a sort. We believe that they saw the feminine principle in the divine, based on findings such as the Venus of Willenorf (from around 30,000 BCE) to examples of goddesses from the Nile region in Egypt such as Nathor figure (from around 4,000 BCE). We assume that the cave paintings and statuary/figurines represent god/goddess images, or their priests/priestesses, however, that is still an assumption. The rites and rituals that may have accompanied these items would have elements of what we know today as witchcraft perhaps evolved with them. At the very least, we can deduce from the artwork that they had religious or spiritual traditions, but what exactly these were in anyone's guess.
It's yet another assumption, but one many are happy to make, that throughout history there have been those who have been seen as different, as set apart from the normal lives and routines of others, whether it be in a tribe or community. These people may have had highly developed sensitivities, and were able to predict the weather perhaps (I personally always know when the pressure is changing from a high to a low front; I can feel it in my head and my ears pop!). They may have had a near-death experience that grants them an ability to deal with death and the dying. They may know where the herbs grow that heal certain wounds. Notice that I say "may" in each of these sentences, because we just don't really know for sure, and it would be irresponsible for me to say otherwise.