Most running injuries are indirectly related to our feet.
It may be because of the way we run and how our foot strikes the ground, or it may be because of the types of shoes we wear while we run.
Sometimes, the problems we may be having are with our feet themselves.
A common complaint that I hear from my athletes are that they have pain or an itchy burning type of sensation above their toes or on the top of their feet.
The first thing that I will lead off with is that I'm a big fan of getting things checked whenever you aren't sure about something.
If there is a local running store that has shoe experts, then you should have them take a look at you and make sure that the shoes are working for you.
Having an expert that you can work directly with is usually the fastest way to find the root cause of any problems that you may be having, either with your equipment or with your biomechanics.
That said, there are a couple of steps that you can take to diagnose and attempt to alleviate the problem.
First, put your shoes on and stand up straight and have somebody check where your toe is in the shoe.
You should have about half of an inch in the toe box in front of your largest toe.
A pain in the top of the foot can often be attributed to the fact that your foot is just far enough outside of the norm that the shoes are pinching a little near the ball of your foot, or else that the shoes you have are just a half of a size too small.
It is not uncommon for one foot to be larger than the other foot, so if you bought shoes sized to your smaller foot then you are certainly likely to have a cramped foot.
If your toe is jammed right up to the front of your shoe, then you need to replace your shoes.
They are just too small.
If you have plenty of room in the toe box and the shoes fit fine, then you may just need to relace your shoes.
An easy way to ease the stress on the painful part of your foot is to lace around the painful areas, rather than over them.
To lace around a problem area:

1. Smear a little lipstick on the top of your bare foot and slide it into your shoe.
   Stand up straight.
   
2. Have somebody press down on the tongue of the shoes over the area that hurts.
   If you do not have somebody handy to help you with this, then you can press down with your other foot.
   
3. Take your foot back out of the shoe and check to see where the lipstick appears on the bottom of the tongue; those are the eyelets that you are going to skip.
   
4. Lace the shoe normally up to the point where it's painful, and instead of crossing over your foot push the shoelace up and through the next eyelet on the same side.
   You'll also want to lace up to the next side on the opposite side of the shoe.
   
5. Resume lacing your shoes normally once you are past the problem areas.
   

What this does is provide a little extra room inside of the shoe so that it will not press in and rub against your foot at the point where it is painful.
This can help relieve enough pressure for the pain to go away and allow you to resume training normally.