Ly, who immigrated from Vietnam in 2008, has been accepted at the University of Pennsylvania for the fall.
At Southern, as the school is called, Ly is known as a humble, intellectual student who scored a perfect 800 on the math portion of his SATs.
"We're proud of him," principal Otis Hackney said. "He's just been an invaluable resource for me as the principal here, in understanding some of the complexities of the issues around South Philadelphia High School."
School officials plan to make an announcement about Ly's award, Hackney added.
The Princeton Prize is awarded annually to one or occasionally two high school students from each of 23 regions around the country. It was established by the university in 2003 "to promote harmony, respect, and understanding" by recognizing students who have a significant, positive effect on race relations.
On Dec. 3, 2009, Southern was rocked by a daylong series of assaults on Asian students carried out by groups of mostly African American classmates. Seven Asian youths went to hospitals and about 50 staged a weeklong boycott.
Last year, the Princeton Prize was awarded to Wei Chen, a boycott leader who demanded accountability from school officials. Ly, then a junior, worked closely with Chen to bring attention to violence issues.
"They're bookends for a phenomenal amount of work around making that school a better place," said Helen Gym, of the advocacy group Asian Americans United, and who works with both youths.
Ly's parents, ethnic Chinese living in Vietnam, fled that Southeast Asian land in 1990, making their way to Thailand. Ly was born there, in a refugee camp, two years later. He was 4 when the United Nations cut off funding for the camps and his family was forced to return to Vietnam.