Promoting Alternatives to Truancy and Incarceration by Encouraging New and Comprehensive Efforts (PATIENCE) Act of 2009 - Amends the Juvenile Justice and Delinquency Prevention Act of 1974 to require the Administrator of the Office of Juvenile Justice and Delinquency Prevention of the Department of Justice (DOJ) to set aside at least 5% of funding under such Act for incentive grants to states. Requires states receiving such grants to: (1) support evidence-based or promising programs that address the mental health treatment needs of juveniles; (2) support reforms that protect juveniles while incarcerated; and (3) demonstrate improvement in public safety and rehabilitation of delinquent and at-risk youth.