Medicare Equity and Fairness in Fee-for-Service Reimbursement Act of 2004 - Amends title XVIII (Medicare) of the Social Security Act, as amended by the Medicare Prescription Drug, Improvement, and Modernization Act of 2003, to direct the Secretary of Health and Human Services to establish a system for making adjustments to the amount of payment made to providers of services and health care professionals for services provided under the original Medicare fee-for-service program, with specified formulae for States whose average per beneficiary amount is: (1) greater than 100 percent of the national average; or (2) less than 100 percent of the national average. Provides for a three year phase-in of such rates.