Short stature and growth retardation is a common condition in children. Genetic variations are responsible for many cases of short stature of unknown etiology. In particular, pathogenic copy number variants (CNVs) have been found in 10%-16% of children with unexplained short stature. This paper reports on a 5-year-old Japanese girl with both growth retardation and developmental delay associated with a 16p13.11 microduplication. Although the patient's mother also carries this microduplication, she did not show growth retardation and developmental delay. These cases illustrate the diverse phenotypic manifestations of 16p13.11 microduplication. Consequently, we conducted the literature review of 274 cases associated with this duplication revealed neurological disorders in approximately 70% of cases, 15.3% of these cases were associated with short stature. Diagnosis of 16p13.11 microduplication remains challenging due to its diverse symptomatology and elusive genotype-phenotype correlations. Comprehensive genetic evaluation is crucial for patients presenting with short stature and developmental disorders, underscoring the need for further investigation into the 16p13.11 microduplication to clarify its specific role and implications.