Epidemiology of stunting in < 5 years old is well characterized; however, its prevalence in adolescence is inconsistent in different geographical locations. We estimated the prevalence of stunting in schoolgirls of Punjab, Pakistan, to standardize local references according to international and national references. 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 analyzed. The 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 local reference for the study population. We used Cohen's kappa statistics to analyze the agreement of our data with reference values, and chi-square test was used as the test of trend. Marked overestimation of the prevalence of stunting was observed (22.72% and 17.49% according to CDC and WHO, respectively) in comparison to local reference (4.94%). According to CDC and WHO references, there was an increasing trend of prevalence of stunting with higher age; however, data was comparable across all the age groups when local references were applied. We recommend that the prevalence of stunting in school-age girls should be determined by applying local height references rather than international ones to plan health strategies and treatments in the local population.