Loneliness is recognized as a significant public mental health issue, especially among adolescents. There is insufficient research on adolescent loneliness in countries such as Kenya, where adolescents make up 23% of the population. The aim of this study was to examine the prevalence of loneliness among high school students living in different regions of Kenya. This cross-sectional study included 2,652 high school students from ten schools across three Kenyan regions, reflecting both urban and rural settings. Participants completed a questionnaire assessing socio-demographic, educational, and psychological factors, along with their experiences of loneliness over the past year. The level of loneliness was assessed by the question “During the past 12 months, how often have you felt lonely?”. Loneliness during the past 12 months (responses “always” and “most of the time”) were identified in 17.1% of males and 16.6% of females. Significant factors associated with loneliness included grade level, geographical location, family structure, and perceived economic status. Urban students and those attending schools in Nairobi and Kiambu, as well as those from economically disadvantaged backgrounds, reported higher loneliness. The high prevalence of loneliness highlights the need for targeted interventions, particularly in urban and economically disadvantaged groups.