Background: There is a scarcity of research in Mongolia that assesses essential minerals—crucial for child growth—by analyzing their levels in hair tissue and correlating these findings with age, gender, and growth indicators. This gap serves as the rationale for the present study. Aim: To determine the prevalence of deficient levels (below laboratory reference ranges) of Na, K, Ca, Mg, Zn, P, Fe, Cu, and Se in hair, and to evaluate their associations with growth curves, age, and gender. Materials and Methods: We conducted a retrospective cross-sectional analysis of data from 1,000 children aged 1–18 years who underwent testing at the “Tod-H” Pediatric Growth Clinic between June 2016 and December 2022. The children were categorized into the following age groups: 0–4 (n=138), 5–9 (n=276), 10–14 (n=390), and 15–18 years (n=196). Mineral analysis of hair samples was conducted at the “Medinex” laboratory in South Korea using the ICP-MS method; values falling below the laboratory’s reference range were classified as a “deficiency.” Among the total of 1,000 children, the growth curves of 997 children with recorded height measurements were evaluated and categorized into three groups: ≤3rd percentile (growth retardation, n=154), 3rd–50th percentile (relatively short stature, n=497), and >50th percentile (normal growth, n=346). Three children diagnosed with autism, for whom height measurement was not possible, were excluded from the growth-related analyses. The prevalence of mineral deficiencies is presented as n (%), and comparisons across growth curve groups, age, and sex were performed using the χ² test, with adjustments made via the Benjamini–Hochberg false discovery rate (FDR) procedure. Logistic regression analysis, adjusted for age and sex, was employed to compare the growth-retarded and relatively short-stature groups against the >50th percentile (normal growth) group. Results: An analysis of mineral levels in the hair of all children included in the study revealed deficiencies (levels below the reference range) in the following proportions: zinc (Zn) in 79.6%, phosphorus (P) in 76.6%, selenium (Se) in 73.3%, calcium (Ca) in 19.7%, and magnesium (Mg) in 17.5%. In the group of children with stunted growth, the prevalence of deficiencies was 88.3% for zinc (Zn), 85.7% for phosphorus (P), and 30.5% for calcium (Ca)—rates higher than those observed in the group of children with relatively short stature (3rd–50th percentiles; Zn 77.9%, P 73.8%, Ca 16.5%) and the group with normal growth (>50th percentile; Zn 78.0%, P 76.3%, Ca 19.7%). After applying the FDR correction, the differences among the three growth-curve groups were statistically significant for Zn (q=0.030), P (q=0.030), and Ca (q=0.006). In contrast, the prevalence of selenium (Se) deficiency was identical across all three growth-curve groups (73.4%, 73.4%, 73.4%; q=1.000). The study results indicate that age-related differences are most pronounced regarding deficiencies in zinc, phosphorus, and calcium. The prevalence of zinc (Zn) deficiency was 99.3% for the 0–4 and 5–9 age groups, 93.6% for the 10–14 age group, and 10.2% for the 15–18 age group. For phosphorus (P), the corresponding figures were 93.5%, 92.8%, 90.8%, and 13.8%, while for calcium (Ca), they were 33.3%, 37.0%, 9.5%, and 6.1%, respectively (p<0.001). Furthermore, the prevalence of deficiencies in zinc (Zn) (84.6% vs. 76.0%; q=0.007), iron (Fe) (5.5% vs. 1.7%; q=0.007), and selenium (Se) (77.4% vs. 70.4%; q=0.049) was higher in females than in males. After adjusting for age and sex and applying the False Discovery Rate (FDR) correction, it was determined that none of the mineral deficiencies showed an independent association with stunted growth or relatively short stature. Conclusion Hair mineral analysis revealed that deficiencies in zinc (Zn), phosphorus (P), and selenium (Se) were the most common. In children with growth retardation, deficiencies in zinc (Zn), phosphorus (P), and calcium (Ca) were relatively more prevalent; however, this was associated with age distribution, and factor analysis did not confirm an independent correlation. Conversely, selenium (Se) deficiency did not differ across the growth curve groups.