In a letter to Congress, Obama said the troops will act as advisers in efforts to hunt down rebel leader Joseph Kony but will not engage in combat except in self-defense.
The White House said the first troops arrived in Uganda on Wednesday. Ultimately, they'll also deploy in South Sudan, the Central African Republic and Congo.
Long considered one of Africa's most brutal rebel groups, the Lord's Resistance Army began its attacks in Uganda more than 20 years ago but has been pushing westward.
Kony is wanted by the International Criminal Court under a 2005 warrant for crimes against humanity in his native Uganda.
Obama's announcement came in low-key fashion -- a letter to the leader of the House, Speaker John Boehner, in which he said the deployment "furthers U.S. national security interests and foreign policy and will be a significant contribution toward counter-LRA efforts in central Africa."
The deployment drew support from Sen. James Inhofe, a Republican who has visited the region.
"I have witnessed firsthand the devastation caused by the LRA, and this will help end Kony's heinous acts that have created a human rights crisis in Africa," he said in a statement. "I have been fervently involved in trying to prevent further abductions and murders of Ugandan children, and today's action offers hope that the end of the LRA is in sight."
But Obama's letter stressed the limited nature of the deployment.
"Our forces will provide information, advice and assistance to select partner nation forces," it said. "Although the U.S. forces are combat-equipped, they will ... not themselves engage LRA forces unless necessary for self-defense."
State Department officials portrayed the deployment as part of a larger strategy to combat the group that dates to the Bush administration but also includes legislation passed by Congress this year.
Victoria Nuland, a department spokeswoman, said the U.S. troops will aid in "pursuing the LRA and seeking to bring top commanders to justice." The broader effort includes encouraging rebel fighters to defect, disarm and return to their homes, she said.
The administration briefed human rights activists ahead of the announcement, and their officials were encouraged.
"These advisers can make a positive difference on the ground by keeping civilians safe and improving military operations to apprehend the LRA's top commanders," said Paul Ronan, director of the group Advocacy at Resolve.