Coal Healthcare and Pensions Protection Act of 2013 - Amends the Surface Mining Control and Reclamation Act of 1977 to address potential shortages in the Multiemployer Health Benefit Plan for payment of health care benefits to retired coal miners by expanding the eligible uses of interest transferable to the plan from the Abandoned Mine Reclamation Fund, and supplemental payments from the General Fund of the Treasury.

Requires calculation of such amount by taking into account only those beneficiaries who are actually enrolled in the plan as of enactment of this Act, as well as those retirees whose health benefits, payable directly by an employer in the bituminous coal industry under a coal wage agreement as a result of a bankruptcy proceeding commenced in 2012, would be denied or reduced.

Requires the Secretary of the Treasury to transfer to the trustees of the 1974 United Mine Workers of America (UMWA) Pension Plan a certain additional amount of funds, to pay pension benefits required under that plan, if the $490 million limitation on certain transfers to the UMWA Combined Benefit Fund and distributions to states and Indian tribes exceeds the aggregate amount required to be transferred to them.

Amends the Internal Revenue Code to prescribe a special rule that employer contributions to an employees' trust or annuity benefit plan providing supplemental benefits solely to participants in a pension plan are neither deductible nor nondeductible as such from the employer's gross income. Subjects such contributions, on the other hand, to deduction as an allowable trade or business expense.

Treats a trust holding the assets of such a pension benefit plan as a tax-exempt organization.

Excludes from taxable wages any payments made to, or on behalf of, an employee or his or her beneficiary under such a plan.