I am not a psychologist or anything in that field, and I have never been afraid of the dark. Just lucky, I guess. However, I will try to be helpful.
My impression from limited reading about conquering phobias is that one can gradually become desensitized. (There is a link to a question on TGO about overcoming phobiassnake-phobias which I added at the end of my answer. See Below.)
The idea is that you confront your fear or aversion, in small steps. For example, in the snake example, you start by looking at photos of snakes, starting with small snakes.
In the case of this questioner, I would suggest starting by running at dusk; next, starting to run at dusk, but timing things so that it is dark when he or she is a short distance from a lighted end-point. Then gradually increase the distance run in darkness, and then turn off the light at the end point.
Another tactic would be to run with a friend a short distance in darkness, then longer distances, and finally alone.
I also suggest the OP figure out under exactly what conditions the darkness is a problem. For example, is the OP uneasy when it is dark inside?
Finally, three points: (1) Experiment, but if the experiments do not help at all after, say, two months (a time I picked in total ignorance of what is reasonable), then seek professional help. (2) There are reasons to be concerned about running in the dark -- tripping, running into something, in some places being mugged -- but these are all entirely rational. So study your route in the daylight. (3) Try to improve your dark adaption, or at least understand at what point things look really dark to you, compared to someone else. I happen to have very good dark adaption, and a flashlight often makes things worse, for me.
I have no idea what will improve your dark adaption, if it is not good. Vitamin A ???? Better glasses ??? This is maybe a separate question.
Addendum: See the following Q and A on overcoming phobias, especially the answer on the Fear Ladder