Homeless Emergency Assistance and Rapid Transition to Housing Act of 2009

Homeless Emergency Assistance and Rapid Transition to Housing Act of 2009 - Amends the McKinney-Vento Homeless Assistance Act to consolidate housing assistance programs for homeless persons.

Declares that the mission of the U.S. Interagency Council on Homelessness is to coordinate the federal response to homelessness and to create a national partnership at every level of government and with the private sector to reduce and end homelessness in the nation while maximizing the effectiveness of federal contributions to end homelessness.

Prescribes requirements for the selection of community homeless assistance planning boards, particularly for collaborative applicants.

Requires the relevant parties in a geographic area to establish a collaborative applicant to apply for a homeless assistance grant. Requires a collaborative applicant to: (1) design a collaborative process to develop such grant applications and evaluate project outcomes; (2) establish priorities for funding projects; (3) participate in the Consolidated Plan for the geographic area served by the applicant; (4) ensure operations of, and consistent participation by, project sponsors in a community-wide homeless management information system (HMIS); and (5) act as a unified funding agency to distribute HUD funds to other project sponsors in the applicable geographic area funds for their projects.

Prescribes requirements for: (1) an emergency solutions grants program; (2) a continuum of care grants program; (3) designation of high-performing communities; and (4) a rural housing stability assistance program.

Increases from 5% to 7.5% the amount of any emergency solutions grant a recipient may use for administrative purposes.

Requires the Comptroller General to study and report to Congress on: (1) appropriate administrative costs for implementing the emergency solutions grants program; and (2) homelessness and homeless assistance in rural areas.