Enhanced Partnership with Pakistan Act of 2009

Enhanced Partnership with Pakistan Act of 2009 - Specifies principles that Congress declares should be the basis of the relationship between the United States and Pakistan.

Authorizes the President to provide assistance to Pakistan to support: (1) democratic institutions; (2) efforts to expand rule of law, build the capacity, transparency, and trust in government institutions, and promote internationally recognized human rights; (3) economic freedom and development; (4) investments in people, particularly women and children; and (5) strengthen public diplomacy to combat militant extremism and promote a better understanding of the United States.

Authorizes FY2010-FY2014 appropriations for assistance to Pakistan under the Foreign Assistance Act of 1961, including: (1) international military education and training (IMET); and (2) foreign military financing for the purchase of defense articles and services, among other things.

Authorizes the Secretary of State to establish an exchange program between military and civilian personnel of Pakistan and certain other countries, including North Atlantic Treaty Organization (NATO) member countries.

Prohibits any security-related assistance and arms transfers to Pakistan during FY2010-FY2014 until the Secretary of State certifies that: (1) Pakistan's government is continuing to cooperate with the United States in efforts to dismantle supplier networks relating to the acquisition of nuclear weapons-related materials; (2) Pakistan's government during the preceding fiscal year has demonstrated a sustained commitment to and is making significant efforts towards combating terrorist groups; and (3) Pakistan's security forces are not materially and substantially subverting Pakistan's political or judicial processes. Provides for a national security waiver of such limits.

Prescribes FY2010 requirements for the Department of State's Pakistan Counterinsurgency Capability Fund.

Restricts the provision of any direct cash security-related U.S. assistance or non-assistance payments to Pakistan to civilian authorities of a civilian government. Provides for a national security waiver of such restriction.

Directs the Secretary to submit a Pakistan Assistance Strategy Report to the appropriate congressional committees. Requires the Comptroller General to review and comment on the Report, and recommend any additional actions that could help improve the efficiency and effectiveness of U.S. efforts to meet the objectives of this Act.

Directs the President to develop and report to the appropriate congressional committees on a comprehensive interagency regional security strategy to eliminate terrorist threats and close safe havens in Pakistan.