Introduction: In Malaysia, the adolescent health studies conducted in 2012 and 2017 revealed an increasing trend of adolescent health risk behaviours and protective factors. This current study aims to determine health risk behaviours and protective factors among adolescents in the country. Methods: The current nationwide cross-sectional study of Malaysian secondary school students used multistage stratified sampling to select 240 nationally representative schools. This study was conducted from June to July 2022 among the students in forms 1, 2, 3, 4, and 5 in all Malaysian states by 34 data collection teams. A validated self-administered questionnaire was used, similar to those used in the NHMS 2012 and NHMS 2017. The quality control was done twice, once at the field level and once at the central level. Sample weighting and analysis were conducted using SPSS statistical software version 28.0. Results: A total of 239 schools out of 240 schools took part in the study (response rate, 99.6%) and total of 33,523 students were involved in this study (response rate, 89.4%). In terms of ethnicity, the highest number of students who participated in the study were Malay (63.0%), followed by Chinese (18.1%) and Indian (6.0 %). While the distribution of sex and form among the students were almost the same. Conclusion To obtain an accurate representation of the nation's adolescent population for this study, samples from public and private schools that are governed by the Ministries of Education and Rural and Regional Development were deemed to be the most reliable.