The settlement was announced Wednesday by the AIDS Law Project of Pennsylvania and the Milton Hershey School, which is financed by a trust that holds the controlling interest in The Hershey Co. candy manufacturer. The settlement is subject to court approval.
The school, for poor and socially disadvantaged students, also must pay $15,000 in civil penalties and provide HIV training for students and staff members.
The Philadelphia-based AIDS Law Project sued the school in federal court last year after it refused to enroll the boy, an honor roll student from the Philadelphia area, on the grounds that he would be a threat to other students' health and safety.
In August, the school reversed its policy and announced it would treat applicants with HIV the same as others.
The school, which has about 1,850 students in pre-kindergarten through 12th grade, also offered to admit the boy, identified in the lawsuit by the pseudonym Abraham Smith, but he and his mother decided he would seek other educational opportunities instead.
The AIDS Healthcare Foundation, which says it provides medical care to people with HIV and AIDS all over the world and contributed money to the boy's cause, welcomed news of the settlement.
"No doubt, advocacy aided this young man's quest for justice," foundation president Michael Weinstein said in a statement.