Highway Fairness and Reform Act of 2009 - Directs the Secretary of Transportation, beginning with FY2011, to carry out a direct federal-aid highway program to permit a state governor or chief executive officer, at least 90 days before the beginning of a fiscal year, to elect to: (1) waive the state's right to receive apportioned or allocated funds under the federal-aid highway program; and (2) receive instead a prorated amount of the taxes appropriated to the Highway Trust Fund (other than from the Mass Transit Account) which are attributable to highway users in the state. Requires a pro rata reduction of such tax-equivalent amount in order to fund contract authority for programs of the National Highway Traffic Safety Administration (NHTSA) and the Federal Motor Carrier Safety Administration (FMCSA).
Requires the Secretary to accept a state's election if: (1) the state has an interstate maintenance program; (2) it submits a plan describing the purposes, projects, and uses to which such amounts will be put and the federal-aid highway programmatic requirements the state elects to continue; (3) the state agrees to obligate program amounts exclusively for projects that would be eligible for surface transportation program funding; and (4) it continues to suballocate surface transportation program funds to urbanized and other areas using certain formulae and rules.