Afghanistan and Pakistan Reconstruction Opportunity Zones Act of 2009

Afghanistan and Pakistan Reconstruction Opportunity Zones Act of 2009 - Declares the purposes of this Act, including to stimulate economic activity and development in Afghanistan and the border region of Pakistan in an effort to combat violent extremism.

Authorizes the President to: (1) designate an area within Afghanistan or Pakistan as a Reconstruction Opportunity Zone, provided such country meets certain eligibility requirements; and (2) proclaim duty-free treatment for certain articles (including certain textile and apparel articles as well as non-textile or non-apparel articles) that are imported into the United States from a designated zone within such country, provided certain requirements are met. Specifies rules of origin for such articles.

Prohibits duty-free treatment for any such articles unless the country in question adopts certain enforcement measures to prevent their unlawful transshipment and the use of false documents relating to importation into the United States.

Authorizes the President to: (1) waive duty-free treatment for such articles if it is inconsistent with the national interests of the United States; and (2) withdraw, suspend, or limit such treatment.