Experiment tweaking your bike. Change one thing at a time, see if it has any effect over a few rides. If not, try changing something else.
Example: I had horrible neck pain while riding which led to migranes. I put some spacers on my stem to raise the angle of my handlebars. It allowed me to sit a little more upright (less aggressive). My neck pain went away very quickly. There was now little stress on my neck, trying to look up while riding.
Perhaps your bike is too long for you, you're stretching too much to get to the handle bars (as an example). Or perhaps your bike is too small and you're cramped on it. Etc.
Good advice earlier in the a post, go to your LBS and have them help fit the bike to you.
Good luck.