Congenital isolated hypogonadotropic hypogonadism refers to a group of predominantly monogenic diseases associated with impaired production, secretion, and/or action of the gonadotropin-releasing hormone (GnRH), which leads to a pronounced delay or absence of puberty. Clinical and genetic heterogeneity is typical of this group of diseases. To date, about 30 candidate genes associated with the development of various forms of secondary hypogonadism are known. Congenital hypogonadotropic hypogonadism can be verified only using molecular genetic diagnostics. The correct diagnosis is necessary for predicting the disease course and choosing the proper approach for managing the patient. We describe a familial case of normosmic hypogonadotropic hypogonadism and late puberty associated with a mutation in the FGFR1 gene. The case is interesting because of pronounced phenotypic manifestations and their high concentration in the proband’s family history. Also of interest is the phenotype untypical of mutations in this gene. The molecular genetic study was performed using new generation sequencing with the authors’ panel of primers and a PGM semiconductor sequencer (Ion Torrent). The Sanger method was used to confirm the identified mutation and examine the proband’s relative. In both patients, a heterozygous mutation in the FGFR1 gene, previously described in Kallmann syndrome, was detected.