Background: Academic performance is concerned with the quantity and quality of learning attained in a subject or group of subjects after a long period of instruction. Excessive stress hampers students’ performance. Improvement in academic performance and alertness has been reported in several yogic studies. Aims and Objectives: The main objective of the study was to assess the effect of yoga on academic performance in relation to stress. Materials and Methods: The study started with 800 adolescent students; 159 high-stress students and 142 low-stress students were selected on the basis of scores obtained through Stress Battery. Experimental group and control group were given pre test in three subjects, i.e., Mathematics, Science, and Social Studies. A yoga module consisting of yoga asanas, pranayama, meditation, and a value orientation program was administered on experimental group for 7 weeks. The experimental and control groups were post-tested for their performance on the three subjects mentioned above. Results: The results show that the students, who practiced yoga performed better in academics. The study further shows that low-stress students performed better than high-stress students, meaning thereby that stress affects the students’ performance.