Background: Epidemiology of stunting in <5 years old is well characterized, however its prevalence in adolescence is inconsistent in different geographical locations. We aimed to estimate the prevalence of stunting in schoolgirls of Punjab, Pakistan according to international and national references, to standardize references and devise strategies to combat stunting in adolescent girls of Punjab, Pakistan.Methods: In this population wide cross-sectional study, 10,050 schoolgirls aged 8-16 years from 12 different districts of northern, central and southern Punjab were analysed. Prevalence of stunting was calculated by applying Centres for Disease Control and Prevention (CDC) and World Health Organisation (WHO) height-for-age references and the national reference for study population. We used Cohen’s kappa statistics to analyse agreement of our data with reference values and chi square test was used as the test of trend.Results: Marked overestimation of prevalence of stunting was observed (22.72% and 17.49% according to CDC and WHO respectively) in comparison to local reference (4.94%). There was an increasing trend of prevalence of stunting with higher age according to CDC and WHO references; however, data was comparable across all the age groups when local references were applied.Conclusion: We recommend that prevalence of stunting in school-age girls should be determined by applying local height reference rather than international ones to plan health strategies and treatments in local population.