The US troops, subject to the approval of national authorities, could also deploy from Uganda into South Sudan, the Central African Republic and Democratic Republic of the Congo, Obama said in a message to Congress.
LRA rebels are accused of murdering, raping and kidnapping thousands of people in those four nations. Tens of thousands of people have died in their 20-year war in northern Uganda.
Obama said the US troops would act as advisors to local forces with the goal of removing LRA leader Joseph Jony and other senior leaders from the battlefield. But he said they would not lead the fighting themselves.
"Although the US forces are combat-equipped, they will only be providing information, advice, and assistance to partner nation forces," Obama said.
"They will not themselves engage LRA forces unless necessary for self-defence. All appropriate precautions have been taken to ensure the safety of US military personnel during their deployment."
The president said a small group of troops deployed on Wednesday and that additional forces would deploy over the next month.
Kony is accused of war crimes and is wanted by the International Criminal Court.
The civil war effectively ended in 2006 when a peace process was launched, but Kony and his top commanders are accused of continuing to commit atrocities in remote areas of neighbouring countries.
General Carter Ham, the head of US Africa Command, said last week that his best estimate was that Kony was probably in the Central African Republic.
Jendayi Frazer, former assistant secretary of state for African affairs in the administration of George W Bush, told Al Jazeera that the LRA had destabilised the region and posed a threat to US allies and American national security.
Kony's men had attacked international peacekeepers and local communities and threatened the newly created nation of South Sudan, Frazer said.
"It's again undermining a nation that the United States is strongly invested in its stability and its democratic progress," she said.[ach/alj]
