Well, I am no pharmacist, but I sleep with one.
Flexeril (Cyclobenzaprine Hydrochloride) is commonly used to treat muscle spasms, not headaches per say. If you cannot workout without experiencing a migraine afterwards, the issue is a bit larger than the headache and treatment may need to expand to include physical therapy to heal your body back to the point where it can handle strenuous exercise without punishing you with a pounding headache. Or, you might end up on meds for your migraines, which would be another lengthy post. I'll skip it.
Quick question -- what else triggers your migraines? Some examples may include: other physical activity, certain foods, when you consume alcohol/smoke cigarettes, stress, etc.
Are you being treated for depression? If so, be certain the doctor prescribing the Flexeril knows this and DO NOT take MAO inhibitors while taking Flexeril, or for up to 14 days afterwards. The interaction of the two has been known to cause death.
DO NOT take more than is indicated on the label. The combination of too much Flexeril and extreme cardiovascular activity could be potentially dangerous.
Stay hydrated, especially if you are being more physically active than you would be normally. Dehydration is going to come quicker and be MUCH more serious while taking your prescription.
It would not be uncommon for you to experience one of the following while taking Flexeril: drowsiness, dry mouth, headache (ironic, ain't it?) and fatigue. You're smart to avoid taking it before a workout.
Ok, back to your question. NO, whether still in your system while working out or taken afterwards, Flexeril isn't likely to impact your body's ability to breakdown and rebuild muscle resulting from your weight training regimen. It's more likely that the true cause of your migraines will do more to hinder your efforts than the drug.
When you see your Doc, discuss the most serious symptom (I assume it's the migraines) and work your way back together. Once you can identify and (ideally) control what's causing the migraines, you'll have a better chance of maintaining your workout routine and seeing progress.
If you'd like to learn more about Flexeril, visit: