Runaway, Homeless, and Missing Children Protection Act

Amends RHYA part A (Runaway and Homeless Youth Grant Program) to provide for an exception to a 20-youth-maximum-capacity requirement for funding a runaway and homeless youth center or a locally controlled temporary shelter if the applicant assures that there is a State or local law or regulation that requires a higher maximum to comply with licensure requirements for children and youth serving facilities.

Includes maternity group homes among the types of transitional living youth projects eligible for grants under part B (Transitional Living Grant Program) of RHYA..

Extends an individual youth's eligibility to remain in a part B shelter beyond the regular 540-day period, until the earlier of the youth's 18th birthday or the 180th day after the end of the 540-day period.

Extends through FY 2008 the authorization of appropriations for programs under: (1) RHYA part E, Sexual Abuse Prevention Program; and (2) all other parts of RHYA. Increases to a minimum 45 percent, and a maximum 55 percent under certain conditions, the part B portion of funds allocated to parts A and B.

Revises RHYA part A coordination assurance and part B coordination agreement requirements to provide for coordinating services with school district liaisons designated the McKinney-Vento Homeless Assistance Act, to assure that runaway and homeless youth are provided information about the educational services available to such youth under such Act. Requires part B plan development to include referral of homeless youth to postsecondary education, to training services and programs under the Workforce Investment Act of 1998, and welfare programs under the Personal Responsibility and Work Opportunity Reconciliation Act of 1996.

Directs the Secretary of Health and Human Services to: (1) report on strategies to end youth homelessness; and (2) evaluate RHYA part B programs to report on long-term housing outcomes for youth 12 to 18 months after exiting the program.

Sets 18 years as the maximum age limit for youth seeking shelter in RHYA part A centers.

Amends MCAA to extend through FY 2008 the authorization of appropriations for: (1) an annual grant by the Administrator of the Office of Juvenile Justice and Delinquency Prevention (in the Department of Justice) to the National Center for Missing and Exploited Children (NCMEC); and (2) other programs under MCAA.

Requires NCMEC to coordinate the operation of a cyber tipline for reporting Internet-related child sexual exploitation in the areas of: (1) distribution of child pornography; (2) online enticement of children for sexual acts; and (3) child prostitution.