This article reports the case of a 15-year-old girl with primary amenorrhea and olfactory dysfunction. Evaluation demonstrated hypogonadotropic hypogonadism, and an initial clinical diagnosis of Kallmann syndrome was made. Whole-exome sequencing identified a novel heterozygous CHD7 variant, c.5238_5239del(p.Tyr1746*), which was classified as likely pathogenic according to the variant interpretation guidelines of the American College of Medical Genetics and Genomics. In light of the typical clinical phenotype and genetic findings, the patient was diagnosed with CHD7-related Kallmann syndrome. This case broadens the CHD7 mutational spectrum in Kallmann syndrome and provides valuable insights to inform clinicians' understanding of this disease.