The present study was aimed to analyze the effects of peer tutoring on the academic achievement of students in the subject of biology at secondary level. The objectives of the study were: (1) To find outthe effect of peer tutoring on the academic achievement of students in the subject of biology; (2) To investigate the effect of peer tutoring on the academic achivement of tutors and tutees of experimental group; (3)To examine the effects of peer tutoring with respect to knowledge, comprehension and application levels of cognitive domain of Bloom Taxonomy; (4) To explore the effect of peer tutoring on the motivation of the students towards learning. All 433,405 boys‟ students at secondary level of 10th grade of Khyber Pakhtunkhwa were the population of the study. Forty (40) students of 10th grade, who were studying biology as elective subjects, were taken as sample of the study from Allied National Software Institute (ANSI), a private secondary school in Mardan through random sampling. The Pretest Posttest Equivalent Group Design was used. Teacher made pretest, posttest and participant observation were the data collection tools. The data collected from pretest and posttest, were analyzed through independent sample t-test and ANOVA. The qualitative data obtained from participants observation, was analyzed qualitatively. It was found that the mean score of experimental group was significantly better than the mean score of control group. It was found through participant observation that peer tutoring had developed strong motivation in both tutors and tutees. It was concluded that peer tutoring was the effective method of instruction of teaching biology at secondary level which had enhanced significantly the academic achievement and motivation of both tutors and tutees as compared to control group. Peer tutoring was also found effective in the development of academic achievement of students at secondary level with respect to knowledge, comprehension and application levels of bloom taxonomy. It was suggested that peer tutoring may be incorporated along with other teaching methodologies of teaching for the subject of biology and due consideration may be given to tutoring strategies in all teacher education practices in the country. The principles, procedures and rules of peer tutoring should be followed while conducting any peer tutoring program. The current study is conducted on male students; therefore, future studies are recommended to use different samples of male and female students at different academic levels.