Defense Department spokesman George Little said Carter met with senior Ugandan military and political leaders to affirm the U.S. commitment to Ugandan defense.
"The deputy also met with U.S. personnel supporting the Ugandan military's effort to remove leaders of the LRA from the battlefield," the spokesman said in a statement Tuesday.
U.S. President Barack Obama in late 2011 deployed 100 military advisers to the region to help military forces take on the LRA.
LRA leader Joseph Kony is the target of a 2005 arrest warrant by the International Criminal Court. His militant group is suspected of conscripting child soldiers and using girls as sex slaves.
Uganda has been monitoring militant activity along its western border with the Democratic Republic of Congo. Ugandan rebel forces fighting in eastern DRC forced thousands of refugees to flee across the border.
Carter is the highest-ranking U.S. Department of Defense official to ever visit Uganda.