Students’ gender differences in mathematics self-concept have important implications for the under-representation of women in science. Typically, students’ gender differences in mathematics self-concept emerge at the beginning of high school which has consequently led to female students performing poorly in the subject in the Kenya Certificate of Secondary Education (K.C.S.E) examinations. That has raised concerns among the stakeholders in education due to the importance attached to mathematics. The factors that are attributed to the female students’ dismal performance in the subject include; poor attitude towards the subject by the students and teachers, gender stereotypes, lack of role models, low mathematics self-concept and the instructional methods used by teachers. This study sought to address the problem of ineffective instruction methods used by teachers and low mathematics self-concept by gender. This is as a result of inadequate information in research conducted in Kenya on effects of the use of Jigsaw Cooperative learning Strategy on students’ self-concept in mathematics by gender. Solomon Four non-equivalent control group design was used in the study. A simple random sample of four co-educational secondary schools was selected from Laikipia County. The sample size was 4 schools out of the possible 67 schools with a population of about 20,800 students in Laikipia County. A mathematics self-concept scale (MSC) for students were used to collect the required data. A total of 183 Form three secondary school students (i.e., 85 girls and 98 boys) filled the MSC questionnaires. The MSC was piloted in a school which was not used in the study in Laikipia County and it’s reliability estimated. The reliability coefficient of the MSC was computed to be 0.96 using Cronbach alpha. Data were analyzed using posttest mean and t-test at alpha (ά) level of .05. The study revealed that gender did not affect students’ mathematics self-concept when students were taught using Jigsaw cooperative learning strategy (t (81) = -1.345, p =.155). The findings are expected to be useful to teachers in secondary schools because they will be able to identify learning strategies which will improve learners’ mathematics self-concept and their achievement in the subject. Curriculum developers and education officers are likely to benefit from this study in deciding on the appropriate learning strategies for learners to improve the quality of mathematics in the country. The research recommends use of Jigsaw cooperative learning strategy in mathematics instruction in secondary schools in Kenya to improve and also reduce gender disparities in the mathematics achievement.