You might consider hypnotherapy.

Music might make things worse, because you're more easily startled by anything that you do hear, such as another runner or a bike coming up from behind. I like to run with music if I'm alone, but don't on country roads because of vehicles sneaking up on me. Even some paths need care. Even in daylight - in fact darkness makes cars more obvious with their lights

If you're in the States, you might consider buying a gun or a weapon of some description

@Valorum That sounds like an absolutely horrible idea, and doesn't even address OP's concern (which is the admitted irrational feelings of fear, not actual fear for their safety).

@chepner "sounds horrid" to people from elsewhere may not be horrid to a USAian mind. (Im in NZ). || In this context it MAY address the OP's concern. || It sounds like a potentially feasible idea. I thought of suggesting a "spoof" weapon. (anti Vampire/... weapon). Irrational fears MAY be addressed by irrational tools.

@RussellMcMahon I am in the US. Nothing in the question suggests the OP feels the need for any kind of defense.

Have you considered/tried running in the morning instead of evening? This can have quite a psychological advantage because it will get lighter and lighter as you run, instead of darker and darker. Of course it does require more discipline to actually get out so early...

If you are into meditation in the nature, you can try to feel that you are one with the surrounding and this is your home. The nature protects you and you protect it. You/we are one. Moreover you are the most dangerous being around. Given that you go to run despite your fears, it sounds like things are not beyond control. Try not to submit to the fear but even slow down or stop and contemplate these ideas. Most likely soon you will desensitize and even feel very good.

This is such a great question. I had a similar experience getting comfortable swimming alone in deep water. It's a great opportunity for self reflection and exploration (it's not easy but it's worth it). Good luck!

Have you tried replacing your irrational fears with rational ones, such as tripping over a root or taking a branch to the face?

@chepner That is not wise. If the OP does need it one day, it would be too late. I would suggest some kind of defensive weapon just in case. That could be a stick, a cane, or whatever easy to carry while running that is legal in the OP's country.

Reduce your audio sensitivity with music is just bad. You will never hear anything approaching from behind or near you. If the OP wants to listen to music while running in the dark, he/she might just as well be using a blindfold.

Whether it's truly a phobia or 'merely' a rational fear, you might a get a money-back guarantee of rescue from many Ericksonian hypnotherapists or NLP practitioners.

FYI, fear of dark is called nyctophobia so you may want to look there. Respectfully as well: would you be comfortable sharing your gender? What might be a safe outdoor activity for a man after dark may unfortunately not necessarily be so for a woman. So the advice given should take that into account.

@chepner I am not intending to be rude. The op said " ... but instead I fear what most would probably consider to be taken from horror movies ... " ->> they know that the fears are irrational. A horror movie defence MAY be addressed by a horror movie style weapon. I think Van Helsing's repeating crossbow rather cool. May not work in dark woods. || (I'm old and have never owned a firearm).

@ItalianPhilosophers4Monica I'm a man. But I am not sure if/how this is relevant to my question as my fears are irrational in nature.

@jng224 Well, seeing as you're a guy, I feel that people have more solid grounds in giving you advice on how to get over those fears and talking down actual risks. I don't think a woman being worried about jogging on trails after dark is an irrational fear, at all. I've generally told my daughter to be mindful of being in parks and forests alone after dark. I don't say that to my son. That's not sexism, it's just safety common sense: it's not fair, but some men do prey on women, in ways that other men are not subjected to.

Btw, nothing "wrong" with having phobias either. I have an irrational fear of heights.