Medlock says the agreement includes a "vague" letter of apology from Hernandez.
The former youth inmate was happy the suit was over. "I've never been the same since what Mr. Hernandez did to me," the alleged victim said in a news release. "I trusted him. He promised to help me get into college, and took advantage of me instead. This case was never about the money for me -- it was about holding Mr. Hernandez accountable. Now I can try to move on with my life."
The Associated Press generally doesn't identify alleged victims of sexual abuse.
Hernandez did not immediately return a call seeking comment. Albert G. Valadez, Hernandez's attorney in the criminal and civil proceedings, said Medlock and his client initially sought $500,000.
"We're glad the case is finally at an end," Valadez said. "John Paul has endured a lot" recently as his mother died earlier in May.
Medlock said the money was all Hernandez had after paying attorney's fees in his criminal trial.
"We're happy to have gotten this measure of justice," he said. "It does send a message that there's going to be accountability in cases like these."
In February, Hernandez was found not guilty of sexually abusing five inmates at the West Texas State School in Pyote in 2004 and 2005. Medlock's client was among the five and all testified against the former principal.
A 2005 report from Texas Rangers investigators said Hernandez summoned young male inmates from their dorms late at night and from classrooms and took them to darkened conference rooms or other areas for sexual encounters.
The case upended the Texas Youth Commission. Lawmakers eventually ordered an overhaul of the system.
Valadez, who also represented Hernandez in the criminal trial, told jurors in his closing argument that once allegations were made against the school's former assistant superintendent, Ray Brookins, it was easy for Hernandez's accusers to say it also happened to them.
In April 2010, Brookins was found guilty of sexually abusing a then-18-year-old inmate in 2004 and sentenced to 10 years in prison.
Both were allowed to quietly resign amid the Rangers' investigation.