National Aviation Capacity Expansion Act of 2003

National Aviation Capacity Expansion Act of 2003 - Declares that if the Federal Aviation Administration (FAA) makes, or at any time after December 5, 2001 has made, a grant to the city of Chicago, Illinois, with the approval of the State of Illinois for planning or construction of runway improvements at O'Hare International Airport, the State of Illinois (including any instrumentality or political subdivision) is prohibited from exercising certain authority to prevent: (1) further consideration by the FAA of the O'Hare airport layout plan (capacity enhancement project for the redesign of the airport's runway configuration) contained in the agreement reached by the State and Chicago on December 5, 2001; (2) construction of projects approved by the FAA in such plan; or (3) application by Chicago for Federal airport improvement program funding for projects approved by the FAA and shown on the plan.

Authorizes Chicago to apply directly to the FAA without the approval of Illinois for Federal airport improvement program funding for planning and construction of a project under the O'Hare airport layout plan.

Makes the FAA Administrator's approval of an airport layout plan submitted by the city of Chicago that includes the runway redesign plan conditional on the meeting of specified requirements.

Requires Illinois to prepare an implementation plan under the Clean Air Act in accordance with the State's customary practices for accounting for and regulating emissions associated with activity at commercial service airports.

Requires the withholding of all airport grant funds for O'Hare (other than grants involving national security and safety) until January 1, 2026, unless specified conditions with respect to operations at Merrill C. Meigs Field have been met.

Expresses the sense of Congress that the Office of Environment and Energy of the FAA should be funded to carry out noise mitigation programming and quiet aircraft technology research and development at specified levels.