Miss. Code § 27-13-47
If the amount already paid under the requirements of this chapter is in excess of the amount determined to be properly due, then the amount of such overpayment shall be credited to the organization, and having been so credited shall be refunded to the extent of its excess over any debts outstanding against the said organization for taxes imposed by this chapter. Such refund shall be effected in the manner provided in Section 27-73-1, Mississippi Code of 1972.
An organization may appeal to the commissioner for a refund of any tax overpayment at any time within three (3) years from the time of said payment and a final determination shall be made in the same manner as is provided in this chapter for appeals from assessments.
Miss. Code § 27-13-47