Federal Courts Budget Protection Act - Rewrites provisions of the Federal judicial code regarding budget estimates for the Administrative Office of the United States Courts. Requires the Director of the Office, under the supervision of the Judicial Conference of the United States, to submit to Congress before January 25 of each year annual estimates of the expenditures and appropriations necessary for: (1) the maintenance and operation of the courts and the Office and the operation of the judicial survivors annuity fund (the Fund) and any supplemental and deficiency estimates as may be required by law for such purposes (requires such estimates to be approved, before presentation to Congress, by the Judicial Conference, with exceptions for the Court of International Trade and for the United States Court of Appeals for the Federal Circuit, which shall be approved by such courts, respectively); and (2) real property construction activities related to U.S. courthouses and other space occupied by entities of the judicial branch. Requires that estimated expenditures and appropriations be based on prospectuses and other information provided by the Administrator of General Services.

Requires the Administrator, at such times as are required by Congress or the judicial branch to ensure timely development and consideration of courthouse needs and budget requests, to prepare and submit directly: (1) to the Director and to specified congressional committees prospectuses, including cost estimates, for future judicial branch construction, acquisition, and repair and alteration projects; and (2) to the Director preliminary planning, design, and cost estimates of future judicial branch construction, acquisition, and repair and alteration projects. Authorizes funds to be appropriated (in accordance with such estimates) to the judicial branch for deposit into the Federal Buildings Fund.

Directs that the estimates submitted to Congress also be submitted to the President for inclusion in the U.S. budget. Prohibits the President from: (1) making any changes in including the estimates in the budget; and (2) imposing or otherwise recommending implementation of a negative allowance, rescission, or any other form of reduction or change to such estimates.

Requires the Director, for the purpose of preparing a unified Federal budget, to transmit to the President: (1) preliminary estimated expenditures and proposed appropriations for the judicial branch before October 16 of each year; and (2) final estimated expenditures and proposed appropriations for the judicial branch before December 24 of each year, which shall be identical to the estimates to be submitted to Congress.

Requires the Director to cause periodic examinations of the Fund to be made by an actuary, whose findings and recommendations shall be transmitted to the Judicial Conference.