No, do not put the amount on your Form 1040. This is allowed when you have two different employers with different EINs.
Instead complete Form 843 to obtain your refund for the overpayment of your social security and medicare tax by the same/one employer/EIN.
Be prepared with the following statement:
Attach a statement from the employer. The statement should indicate the following.
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The amount, if any, the employer has repaid or reimbursed you for excess taxes withheld.
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The amount, if any, of credit or refund claimed by the employer or authorized by you to be claimed by the employer.
The employer should include in the statement the fact that it is made in support of your claim for refund of employee tax paid by the employer to the IRS.
If you cannot obtain a statement from the employer, you should attach a statement with the same information to the best of your knowledge and belief and include in the statement an explanation of why you could not obtain a statement from the employer. Attach a copy of your Form W-2 to prove the amount of social security, Medicare, or RRTA tax withheld.
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