After TM was introduced to the students, Mackay said anxiety levels were reduced, arguments at home and school quelled and even drug use -- especially marijuana -- dropped.
"It just lowers the tension level," he said. "You can notice it."
John Izere, one of his students, arrived two years ago after attending a large school where he routinely got into fights.
The 19-year-old, who arrived in the United States in 1994, is a refugee from Rwanda where he witnessed genocide.
"Every time I heard anything loud like firecrackers, my heart used to drop and I found myself running, even if I was safe," Izere told ABCNews.com.
Since he started practicing TM, Izere's flashbacks have diminished and his school work has improved.
"It helps me with a lot of things I have in my head," Izere said. "It helps me relieve stress and concentrate and focus. It also helps me with my schoolwork and puts me in a good mood and gives me a good day."
When Izere graduates in May with plans to be an engineer, he said he will continue meditating.
"It's not a choice," he said. "It's a must for me."
At-risk students have complicated and stressful personal lives, according to Denise Gerace, program director for the Tucson Transcendental Meditation Center, which is funded by the Lynch foundation.
"But with transcendental meditation, they find more personal clarity and strength to deal with these issues," she told ABCNews.com. "They work out their problems by talking, rather than hitting."
"If a person has limited academic ability and a bad temper, they won't go very far," Gerace said. "But if their temper is under control and they work life out, there is more potential for accomplishment. Their path of life is organized."
But some misperceptions stand in the way of more public schools embracing TM -- not only its association with the '60s, but its religious origins in eastern religion.
In 1979 a federal court in New Jersey outlawed the practice because of First Amendment concerns. And as recently as 2006, parents at Terra Linda High School in California protested a meditation program claiming it was religious in nature, and funding was withdrawn.
But meditation advocates say those attitudes are changing as schools look for better ways to teach their students.
"It's a mechanical technique," Gerace said. "The idea that it's religious is left over from 50 years ago, when it was possible to disregard contributions from somewhere else by simply saying it must be a religious practice."
And Lynch who has three children of his own -- including a 16-year-old -- understands the importance of TM in today's stressful and violent school culture.
"You can kiss stress away," Lynch said. "You see these dogs who come out of the water and they shake all the water off. The stress just flies off."
ABC's information specialist Gerard Middleton contributed to this report.