Limits, beginning in FY2010, certain military assistance and arms transfers to Pakistan until the Secretary of State certifies that Pakistan's security forces: (1) are making concerted efforts to prevent al Qaeda, the Taliban, and other terrorist groups from operating in Pakistan's territory; and (2) are not materially interfering in Pakistan's political or judicial processes. Provides for a national security waiver of such limits.

Expresses the sense of Congress that coalition support funds are critical components in the fight against terrorism.

Directs the Secretary to: (1) develop a comprehensive, cross-border strategy for working with the government of Pakistan, the government of Afghanistan, the North Atlantic Treaty Alliance (NATO), and other allies to implement effective counterterrorism and counterinsurgency measurers along the border areas of Pakistan and Afghanistan; and (2) submit a related report to the appropriate congressional committees.

Expresses the sense of Congress that the United States should: (1) recognize the bold political steps the Pakistan electorate has taken to elect a new civilian government; (2) expand its engagement with the government and people of Pakistan in areas of particular interest and importance to the people of Pakistan; and (3) continue to build a reciprocal security relationship with Pakistan.

(Sec. 5) Authorizes FY2009-FY2013 appropriations for assistance to Pakistan under the Foreign Assistance Act of 1961. States that specified funds should be obligated for police reform and equipping.

Prohibits funds from being made available to Pakistan unless the Pakistan Assistance Strategy Report has been submitted to the Senate Committees on Appropriations and Foreign Relations and the House Committees on Appropriations and Foreign Affairs (Committees).

Limits funds to Pakistan after FY2009 unless the President's Special Representative to Afghanistan and Pakistan certifies to the Committees that assistance to Pakistan has made or is making substantial progress toward achieving U.S. assistance objectives.

Authorizes the Secretary of State to waive such funding restrictions for reasons of U.S. national security.

Expresses the sense of Congress that: (1) subject to an improving political and economic climate in Pakistan specified FY2014-FY2018 funds should be authorized for Pakistan; (2) security assistance should be provided in close coordination with the government of Pakistan and be geared toward bolstering counterinsurgency capabilities to defeat the Taliban-backed insurgency and deny popular support to al Qaeda and other Pakistan-based foreign terrorist organizations; and (3) the government of Pakistan should allocate a greater portion of its budget to education, health, and other priorities described in this section.

Provides that funds should be used for projects to benefit the people of Pakistan, including projects that promote: (1) democratic governance, police reform, and anticorruption efforts; (2) judicial enhancement; (3) efforts against the narcotics trade; (4) economic freedom and growth; (5) investments in people, and particularly, women and children; (6) education and public health; and (7) regional development.

Encourages the utilization of Pakistani firms and community and local nongovernmental organizations in Pakistan to provide such assistance.

Authorizes the use of funds for operational and audit expenses.

Sets forth notification and Pakistan Assistance Strategy Report and Government Accountability Office (GAO) reporting requirements.

Directs the President to consult with the Committees regarding assistance and policy strategies not later than 15 days before obligating any assistance under this section.

(Sec. 6) Limits certain military assistance (as of FY2010) and arms transfers (as of FY2012) to Pakistan until the Secretary certifies to the Committees that Pakistan's security forces: (1) are making concerted efforts to prevent al Qaeda and the Taliban and their associated groups from operating in, or basing attacks into Afghanistan from, Pakistan's territory; and (2) are not materially interfering in Pakistan's political or judicial processes.

Authorizes the Secretary to waive such funding restrictions for reasons of U.S. national security.

Directs the Secretary to report annually to the Committees regarding the progress of Pakistan's security forces.

(Sec. 7) Expresses the sense of Congress that: (1) coalition support funds are critical components of the global fight against terrorism and the primary support for military operations of the government of Pakistan to destroy the terrorist threat; (2) the Pakistan reimbursement claims process for coalition support funds requires increased oversight and accountability; (3) more specific guidance should be generated for officials associated with counterterrorism program oversight within the U.S. Embassy in Pakistan, the United States Central Command, the Department of Defense (DOD), the Department of State, and the Office of Management and Budget (OMB); and (4) the Secretary of Defense should report semiannually to the Committees and to the House and Senate Armed Services Committees on the use of Coalition Support Funds.

(Sec. 8) Directs the Secretary to: (1) develop a comprehensive, cross-border strategy for working with the government of Pakistan, the government of Afghanistan, the North Atlantic Treaty Alliance (NATO), and other allies to implement counterterrorism and counterinsurgency measurers along the border areas of Pakistan and Afghanistan; and (2) submit a related report to the Committees.

(Sec. 9) Expresses the sense of Congress that the United States should: (1) recognize the bold political steps the Pakistan electorate has taken to elect a new civilian government; (2) expand its engagement with the government and people of Pakistan in areas of particular interest and importance to the people of Pakistan; (3) continue to build a reciprocal security relationship with Pakistan; and (4) explore means to utilize the expertise of the Pakistani-American community.

(Sec. 10) States that with specified exceptions this Act shall remain in force after September 30, 2013.

Enhanced Partnership with Pakistan Act of 2009 - (Sec. 4) States that it is U.S. policy to: (1) support the consolidation of democracy in Pakistan; (2) build a long-term relationship with Pakistan; (3) further the economic development of Pakistan by expanding bilateral engagement with the government of Pakistan; (4) work with Pakistan and the countries bordering Pakistan to facilitate regional peace; (5) work with the government of Pakistan to prevent Pakistani territory from being used as a base or conduit for terrorist attacks; (6) expand people-to-people engagement between the United States and Pakistan through increased educational, technical, and cultural exchanges; and (7) encourage the development of local capacity to measure the progress of donor expenditures and better hold the government of Pakistan accountable for fund expenditures.

(Sec. 5) Authorizes FY2009-FY2013 appropriations for assistance to Pakistan under the Foreign Assistance Act of 1961. States that specified funds should be obligated for police reform and equipping.

Prohibits funds from being made available to Pakistan unless the Pakistan Assistance Strategy Report has been submitted to the Senate Committees on Appropriations and Foreign Relations and the House Committees on Appropriations and Foreign Affairs (Committees).

Limits funds to Pakistan after FY2009 unless the President's Special Representative to Afghanistan and Pakistan certifies to the Committees that assistance to Pakistan has made or is making substantial progress toward achieving U.S. assistance objectives.

Authorizes the Secretary of State to waive such funding restrictions for reasons of U.S. national security.

Expresses the sense of Congress that: (1) subject to an improving political and economic climate in Pakistan specified FY2014-FY2018 funds should be authorized for Pakistan; (2) security assistance should be provided in close coordination with the government of Pakistan and be geared toward bolstering counterinsurgency capabilities to defeat the Taliban-backed insurgency and deny popular support to al Qaeda and other Pakistan-based foreign terrorist organizations; and (3) the government of Pakistan should allocate a greater portion of its budget to education, health, and other priorities described in this section.

Provides that funds should be used for projects to benefit the people of Pakistan, including projects that promote: (1) democratic governance, police reform, and anticorruption efforts; (2) judicial enhancement; (3) efforts against the narcotics trade; (4) economic freedom and growth; (5) investments in people, and particularly, women and children; (6) education and public health; and (7) regional development.

Encourages the utilization of Pakistani firms and community and local nongovernmental organizations in Pakistan to provide such assistance.

Authorizes the use of funds for operational and audit expenses.

Sets forth notification and Pakistan Assistance Strategy Report and Government Accountability Office (GAO) reporting requirements.

Directs the President to consult with the Committees regarding assistance and policy strategies not later than 15 days before obligating any assistance under this section.

(Sec. 6) Limits certain military assistance (as of FY2010) and arms transfers (as of FY2012) to Pakistan until the Secretary certifies to the Committees that Pakistan's security forces: (1) are making concerted efforts to prevent al Qaeda and the Taliban and their associated groups from operating in, or basing attacks into Afghanistan from, Pakistan's territory; and (2) are not materially interfering in Pakistan's political or judicial processes.

Authorizes the Secretary to waive such funding restrictions for reasons of U.S. national security.

Directs the Secretary to report annually to the Committees regarding the progress of Pakistan's security forces.

(Sec. 7) Expresses the sense of Congress that: (1) coalition support funds are critical components of the global fight against terrorism and the primary support for military operations of the government of Pakistan to destroy the terrorist threat; (2) the Pakistan reimbursement claims process for coalition support funds requires increased oversight and accountability; (3) more specific guidance should be generated for officials associated with counterterrorism program oversight within the U.S. Embassy in Pakistan, the United States Central Command, the Department of Defense (DOD), the Department of State, and the Office of Management and Budget (OMB); and (4) the Secretary of Defense should report semiannually to the Committees and to the House and Senate Armed Services Committees on the use of Coalition Support Funds.

(Sec. 8) Directs the Secretary to: (1) develop a comprehensive, cross-border strategy for working with the government of Pakistan, the government of Afghanistan, the North Atlantic Treaty Alliance (NATO), and other allies to implement counterterrorism and counterinsurgency measurers along the border areas of Pakistan and Afghanistan; and (2) submit a related report to the Committees.

(Sec. 9) Expresses the sense of Congress that the United States should: (1) recognize the bold political steps the Pakistan electorate has taken to elect a new civilian government; (2) expand its engagement with the government and people of Pakistan in areas of particular interest and importance to the people of Pakistan; (3) continue to build a reciprocal security relationship with Pakistan; and (4) explore means to utilize the expertise of the Pakistani-American community.

(Sec. 10) States that with specified exceptions this Act shall remain in force after September 30, 2013.