Lord's Resistance Army Disarmament and Northern Uganda Recovery Act of 2009 - (Sec. 4) Directs the President to submit to Congress a regional strategy to guide U.S. support for multilateral efforts to eliminate the threat to civilians and regional stability posed by the Lord's Resistance Army (LRA). Requires the strategy to include: (1) a plan to help strengthen efforts by the United Nations (U.N.) and regional governments to protect civilians from attacks by the LRA; (2) an assessment of viable options through which the United States could help develop and support multilateral efforts to eliminate the threat posed by the LRA; (3) an interagency framework to plan, coordinate, and review diplomatic, economic, intelligence, and military elements of U.S. policy across the region regarding the LRA; (4) a description of the type and form of diplomatic engagement across the region undertaken to coordinate and implement U.S. policy regarding the LRA and to work multilaterally with regional mechanisms, including the Tripartite Plus Commission and the Great Lakes Pact; and (5) a description of how this engagement will fit within the context of broader efforts and policy objectives in the Great Lakes Region.

(Sec. 5) Authorizes the President to provide additional assistance to respond to the humanitarian needs of populations the Democratic Republic of Congo, southern Sudan, and Central African Republic affected by LRA activity.

(Sec. 6) Expresses the sense of Congress that the President should support efforts by the people of northern Uganda and the government of Uganda to: (1) assist internally displaced people in transition and returnees by spurring economic revitalization and advancing access to basic services at return sites; (2) enhance the accountability and administrative competency of local governance institutions and public agencies in northern Uganda; (3) strengthen the operational capacity of the civilian police and the justice system in northern Uganda; (4) establish mechanisms for the disarmament and reintegration of former combatants and those abducted by the LRA; and (5) promote programs to address psychosocial trauma.

Expresses the sense of Congress that: (1) the Secretary of State and the Administrator of the United States Agency for International Development (USAID) should work with Congress to increase future assistance to Uganda if the government of Uganda demonstrates a commitment to reconstruction in war-affected areas of northern Uganda; and (2) the Secretary should withhold non-humanitarian assistance to Uganda if the government of Uganda is not committed to reconstruction and reconciliation in the war-affected areas of northern Uganda and is not taking steps to ensure this process moves forward in a transparent and accountable manner.

(Sec. 7) Expresses the sense of Congress that a continued failure to take meaningful steps toward national reconciliation and accountability risks perpetuating political grievances and fueling new conflicts.

Authorizes the President to support efforts by the people of northern Uganda and the government of Uganda to promote transitional justice and reconciliation on both local and national levels, including to encourage implementation of the mechanisms in the Annexure to the Agreement on Accountability and Reconciliation between the government of Uganda and the LRA.

(Sec. 8) Directs the Secretary to report to Congress on implementation of the strategy and evaluation of the assistance under this Act.

(Sec. 9) Expresses the sense of Congress that: (1) of the total amounts to be appropriated for FY2011 for the Department of State and foreign operations, up to $10 million should be used to carry out activities under section 5; and (2) of the total amounts to be appropriated for FY2011-FY2013 for the Department of State and foreign operations, up to $10 million in each such fiscal year should be used to carry out activities under section 7.

(Sec. 10) Defines: (1) "Great Lakes Region" as the region comprising Burundi, Democratic Republic of Congo, Rwanda, southern Sudan, and Uganda; and (2) "LRA-affected areas" as those portions of northern Uganda, southern Sudan, northeastern Democratic Republic of Congo, and southeastern Central African Republic affected by the LRA.
Output: A bill to support stabilization and lasting peace in northern Uganda and areas affected by the Lord's Resistance Army through development of a regional strategy to support multilateral efforts to successfully protect civilians and eliminate the threat posed by the Lord's Resistance Army and to authorize funds for humanitarian relief and reconstruction, reconciliation, and transitional justice, and for other purposes.