I suffer from chronic headaches, and have found that when I stop to rest/meditate ect, they seem to get worse at first.

I have a couple thoughts about how it works for me (maybe for you too):
1. when I stop doing stuff, its only then I realize how busy my brain has been working - so my headache increases
2. It takes time for a busy brain to settle down. If I rest for half an hour, it dies down.
3. You can use methods to try to deal with the pain, but I've been told my multiple doctors that the pain is a symptom of an over worked brain. My brain is working far harder to deal with all the stimulation it has received, and it can take time for it to settle down afterwards.

One thing that can help is limiting unneeded stimulation. Do you know what triggers your headaches? Sounds, complex visuals (looking out a car window while its driving, watching a fast paced movie, ect), physical activity? Maybe limiting whatever your triggers are before you plan to meditate