Background Adolescence is a critical transition in human growth and adolescents tend to engage in various risky behaviors which are likely to continue into adulthood. Co-occurrence of non-communicable disease risk factors has the potential to increase risks of chronic disease comorbidity and increased mortality in later life. Behavioral risk factors are adopted due to changes in lifestyle and adolescents are more prone to acquire them. This study aimed to determine the prevalence and associated factors of co-occurrence of non-communicable disease risk factors among school-going adolescents of Kathmandu Metropolitan City. Methods We conducted a cross-sectional study among school-going adolescents of Kathmandu Metropolitan City in January/February 2020. We used stratified random sampling to select 1108 adolescents studying in 9, 10, 11, and 12 grades. We used Global Schools Health Survey tools to collect data. We entered data in EpiData 3.1 and exported it into Statistical Package for Social Science (SPSS) version 20 for statistical analysis. We estimated prevalence of NCDs risk factors and co-occurrence of risk factors. We applied multivariate multinomial logistic regression analysis adjusting for age, gender, ethnicity, religion, education, type of school, and parental education to determine factors associated with co-occurrence of NCDs risk factors. Results The prevalence of physical inactivity, unhealthy diet, harmful use of alcohol and tobacco among school-going adolescents were 72.3% (95%CI: 69.6–74.9), 41.1% (95%CI: 38.2–44.0), 14.8% (95%CI: 12.8–17.0) and 7.8% (95%CI:6.3–9.5) respectively. The adolescent with co-occurrence of two or more risk factors was 40.7% (95%CI: 37.8–43.7). The school-going adolescents who were in higher age group (AOR = 1.72, 95% CI- 1.06, 2.77), Hindus (AOR = 1.78, 95% CI-1.09, 2.89), other than Brahmin/Chhetri by ethnicity (AOR = 2.11, 95% CI-1.39, 2.22) and with lower education level of mothers (AOR = 2.40, 95% CI- 1.46,3.98) were more likely to have co-occurrence of NCDs risk factors after adjusting for all socio-demographic variables. Conclusion The co-occurrence of non-communicable disease risk factors was high among school going adolescents and was associated with age, religion, ethnicity and mother’s education. Integrated and comprehensive interventional programs should be developed by concerned authorities.