Fuel Supply Improvement Act of 2005

Fuel Supply Improvement Act of 2005 - Prescribes guidelines to expedite federal permitting procedures for construction or expansion of a domestic petroleum refining facility.

Applies such expedited permit procedures exclusively to permits under specified environmental protection statutes.

Directs the Secretary of Energy, upon applicant request, to provide direct legal representation to a refining facility applicant to defend against a lawsuit regarding the permit approval procedure, or facility construction or expansion, if the Secretary believes the lawsuit is without merit, is brought solely to delay facility completion, or will have the effect of delaying facility completion in a period when U.S. domestic refining capability is insufficient.

Instructs the Secretary to establish an office of regulatory assistance whose sole purpose is to assist applicants with permit applications, planning, and otherwise pursuing the construction or expansion of a domestic petroleum refining facility.

Grants the Secretary contracting authority with sponsors of new large-sized petroleum refining facilities.

Establishes in the Department of Energy the Refinery Standby Support Program Account and the Refinery Standby Support Grant Account to cover loan costs and costs resulting from certain construction delays.

Amends the Clean Air Act to direct the Administrator of the Environmental Protection Agency to provide within new source review regulations that equipment replacement shall be considered routine maintenance and repair if it: (1) does not increase actual emissions of any air pollutant by more than 5%; and (2) does not increase actual emissions of any air pollutant by more than 40 tons per year.

Directs the Secretary of the Interior to charge a discounted price in any sale to a qualified small refinery of crude oil obtained by the United States as royalty-in-kind.