Having researched online and found out that I am exempt from paying Social Security and Medicare taxes, I am attempting to follow the advice to ask for a refund from my employer. But how exactly are they meant to do this?

My employer pays for an outside company to deal with our payroll. I spoke with that company today and they said that they could make the changes and refile, claiming the tax back, but said it would cost them $300 or more to do so.

I'm lost. Should my employer state that they can't refund the money and I just file the form 843?

Thanks for any help you can provide.

-EC

What visa do you have? When did you enter U.S. Did you file 2009 tax return? If yes, which form? Without answers to these question, it is not possible to provide proper answer.
You may read this about filing Form 843: Your U.S. Tax Return: Social Security and Medicare (FICA) Taxes for Non-resident Exempt Individual

I am on an F-1 visa, I have only been in the US for two and half years. I filed a 2009 tax return, 1040nr-ez.

From what I gather, I am not required to pay FICA taxes. If this is indeed correct, how is the employer mean to refund this money to me, as suggested by the IRS website..

Yes, on F-1 you are nonresident for 5 years. You must file nonresident tax return and your income is not subject to social security and medicare taxes. For 2009, you can file Form 843 with required documents.
For 2010, you must file your tax return. Wait for 8 weeks and then file Form 843.
For 2011 make sure that your employer does not withhold FICA taxes while you are on F-1 or OPT.

This is most useful. Very much appreciated, thank you.

Last question. If I claim back my SS and Medicare taxes for the years that I was exempt, does it matter in the future if I look to become a permanent resident of the United States? Or will my years on F-1 and OPT always be deemed as exempt, regardless of what happens to my status in the future?

I guess in short, I'm worried that in the future, I will have to pay BACK this money should I ever become a permanent resident.

Hope this makes sense. Thanks.

-EC

F-1 and OPT always be deemed as exempt, regardless of what happens to my status in the future.