While you cannot be denied other legal rights due to taking FMLA status, and your employer cannot legally interfere with your rights under the Act, there can be impacts to your career. If being out of work a certain number of days means you don't meet certain performance goals, you may not receive the promotions or benefits that would come from meeting those goals. However, the same would be true if you worked while sick and couldn't meet the goals, and you're certainly better off in terms of your career than if you had to stop working altogether!
If you need to take time off due to Migraines, it is best to use your paid sick time (might as well get paid!) and then apply for FMLA status if you work for a large enough company. It is always better to let your employer know why you need the time off and make a record in case of the need to apply for disability or to take legal action in the future.
Some employers are suspicious of intermittent FMLA leave. While they will grant the status for fear of lawsuits and EEOC intervention, they will oversee it rigorously. FMLA Online, an HR blog, cautions employers that there is "rampant intermittent FMLA abuse," people who are trying to use FMLA status to beat the system at their employer's expense, citing for example:
Stories like this: A nurse who gets migraines and needs time off on Fridays, Mondays and the day before or after a legal holiday.
FmlaOnline.com, "FMLA Intermittent Leave: Don't Let Employees Beat the System".
I share this not to scare you out of applying for the status, but to prepare you that it may not be easy. There probably are people who abuse the system. There are also many misconceptions about Migraine and chronic illness. You may face all of those when you apply.
You may need to educate your employer about Migraine disease or your other chronic condition. Some employers will be more or less compassionate and enlightened than others. Their bottom line will always be the bottom line - what do you bring to the company, what do you contribute. They will want to comply with the law, they may want to help you as well, but their first concern will be the integrity of their organization. Try to give them as much information as you can, and to show your concern for the job and the organization, and it may make your way easier.
~This sharepost is legal education, not legal advice. No attorney-client relationship is created.~