Stunting remains a major public health concern in Southeast Asia, and is shaped by a complex interplay of genetic, inflammatory, and nutritional factors. This scoping review sought to map genetic polymorphisms associated with stunting in Southeast Asian children and to identify candidate biomarkers for early diagnosis and biologically targeted interventions. Following the Arksey and O'Malley framework and the PCC (Population, Concept, Context) model, a systematic search was conducted across 7 databases. Eligible studies were peer-reviewed, published in English from 2015–2024, involved children under 18 years of age, and investigated gene variants in relation to stunting. A total of 902 records were screened independently by 3 reviewers using predefined criteria, with consensus procedures to resolve any discrepancies. Eleven studies met the final inclusion criteria. Thematic analysis and protein-protein interaction mapping revealed that 5 key polymorphisms—IGF1R, GHSR, MTRR, CASP1, and CARD17—were significant contributors to growth impairment. IGF1R polymorphisms were associated with a 2.46-fold increase in stunting risk (odds ratio [OR], 2.46; 95% confidence interval [CI], 1.60–3.78), while MTRR< variants yielded an OR of 1.93 (95% CI, 1.22–3.05). Similarly, GHSR and CASP1 polymorphisms were linked to increased odds of stunting (OR, 2.15; 95% CI, 1.38–3.34 and OR, 1.67; 95% CI, 1.10–2.54, respectively). These polymorphisms were consistently associated with disrupted growth hormone signaling, chronic inflammation, and nutrient-sensitive pathways. The biological network underlying stunting in this population points to a converging mechanism of impaired endocrine function and inflammatory dysregulation. However, this review’s scope is limited by underrepresentation of some Southeast Asian nations and exclusion of non-English literature. Early genetic screening for high-risk biomarkers and precision-driven nutritional interventions may offer more effective strategies to reduce the burden of stunting in Southeast Asian children.