Secure Trains Act

Secure Transit and Rail Across America and Invest in National Security Act of 2005, or the Secure Trains Act - Directs the Secretary of Homeland Security to: (1) submit to Congress the National Strategy for Transportation Security within 30 days after enactment of this Act; and (2) develop certain supplemental requirements, including prioritized recommendations for improving public transportation and railroad security.

Authorizes the Secretary to make grants to improve the security of public transportation systems against acts of terrorism.

Directs the Secretary to: (1) report to owners, operators, and providers of public transportation systems and specified others on best practices for the security of public transportation systems; (2) develop a national plan for public outreach and awareness of measures the public can take to increase such security; and (3) establish National Transportation Security Centers at institutions of higher education.

Sets forth certain whistleblower protections for Department of Homeland Security employees and federal contractors or subcontractors who provided information or otherwise assisted in an investigation of violations of any law or regulation related to national or homeland security, filed or participated in a proceeding related to such violation, or refused to violate or assist in the violation. Sets forth civil and criminal penalties for violations of such protections.

Authorizes the Secretary to make grants for freight and passenger rail (including hazardous materials transportation) security upgrades.

Authorizes appropriations for Amtrak for certain fire and life-safety improvements to specified tunnels along the Northeast Corridor.

Establishes a research and development (R&D) program to improve railroad security.

Requires the Secretary to issue guidelines for a rail worker security training program.

Sets forth certain whistleblower protections for rail employees or other persons providing information about perceived security threats.

Directs the Secretary to: (1) analyze the cost and feasibility of requiring security screening for passengers, baggage, and cargo on passenger trains; (2) issue certain emergency responder training standards; and (3) provide grants to the Operation Respond Institute.