This is the first published qualitative assessment of a yoga program applied in a high school setting. This qualitative interview study was nested in a randomized, controlled trial studying the effects of a yoga program offered in place of a semester of physical education classes at a rural public high school. Student interviews were conducted after taking part in a semester of the yoga program. A formal passive consent with information about the qualitative study was sent home to parents/guardians of all students in the parent study before the interviews. Most students enjoyed the yoga classes and felt benefits. Negative reports of yoga practice were associated with gender as most males sensed peer pressure against practicing yoga. Despite this finding, most students wanted to continue yoga and would continue if it were offered in school. Positive reports include a greater kinesthetic awareness, which some students associated with a greater respect for the body and improved self-image. Among students reporting psychological benefits, many cited stress reduction; many used yoga to manage negative emotions; and some propagated more optimism. Most thought yoga could reduce interest in the use of drugs and alcohol and increase social cohesion with family and peers. We found that a yoga program is feasible in this sample of 9th and 10th graders, especially after benefits are perceived. We also found evidence that yoga may lead to emergent positive benefits in health behaviors not directly prescribed by the program. These results suggest that school-based yoga programs may be appropriate for promoting healthy behaviors at a societal level by focusing on the prevention of negative patterns during the adolescent transition.