The purpose of this study was to investigate WhatsApp usage and wellbeing of students in mixed secondary schools at Masinga Sub County in Machakos County, Kenya. The study was guided by four research questions focusing on; what is the prevalence of WhatsApp usage among students, what is the prevalence of students’ psychological wellbeing in connection with depression, anxiety and stress, what are the effects of WhatsApp usage on students’ psychological well-being, and What are the strategies used to improve WhatsApp usage among students in mixed secondary school students at Masinga Sub County in Machakos County, Kenya. The study was founded on Generalist Intervention Model and System Theory. The study adopted convergent mixed method research design. The target population was 51 deputy principals, 782 teachers, and 3360 form two students. Systematic sampling was used to sample 10 schools, purposive sampling technique was used to select 10 deputy principals, simple random to sample 156 teachers, and stratified and simple random sampling technique was applied to sample 360 form-two students. Questionnaire and interview guide were used for data collection. Field data was analyzed and presented in tables, frequencies and percentages. The study findings may be meaningful to policy makers, students, teachers and local communities in the sub county as key stake holders. Findings show that WhatsApp usage among the students is widespread in mixed secondary schools. There is a strong significant relationship between students’ WhatsApp use and students’ psychological well-being (r = 0.779, p value =0.001). Changes in WhatsApp usage would predict changes in students’ psychological well-being. The study recommends that; school administrators should put in place stringent strategies to control the use of social media among secondary school students and Ministry of Education should develop policies for curbing the use and challenges associated with social media by secondary school students Keywords: Kenya, Machakos County, anxiety disorder; Mental health; Peer pressure; social media; WhatsApp Messenger