Introduction Adolescence is a time of significant physical and emotional change, and there is emerging concern that adolescents living in low- and middle-income countries (LMIC) may face substantial challenges in relation to linear growth and mental health. Data on the global burden of stunting after 5 years of age are limited, but estimates suggest up to 50 per cent of all adolescents in some LMIC are stunted. Additionally, many LMIC lack robust mental health care delivery systems. Pakistan has one of the world's largest populations of adolescents (10 to 19 years) at approximately 40 million. The Nash-wo-Numa study's primary objective is to assess the prevalence and risk factors for stunting among early adolescents in rural Pakistan. The study also aims to determine the prevalence of poor mental health and identify factors associated with common mental health concerns during the childhood to adulthood transition. Methods This cross-sectional study will include girls (n= 738) 9.0 to 14.9 years of age and boys (n=687) 10.0 to 15.9 years of age who live in the rural district of Matiari, Pakistan. Participants will be assessed for anthropometrical measures, puberty development, nutritional biomarkers as well as symptoms of depression, anxiety and trauma using validated scales. Ethics and dissemination The proposed study aims to complete the picture of child and adolescent health concerning linear growth and mental health by including puberty indicators. Ethics approval has been granted by the Ethics Review Committee at the Aga Khan University, Karachi, Pakistan, #5251-WCH-ERC-18 and Research Ethics Board at SickKids Hospital, Toronto, Canada, #:1000060684. Study results will be presented at relevant conferences and published in peer-reviewed journals. Trial registration number NCT03647553; Pre-results.