This report details a case of a female patient with genetically confirmed Kallmann syndrome, which was found to be related to a novel molecular variant of the FGFR1 gene. We present a case of a 12-year-old girl, referred to the Pediatric and Adolescent Gynecology Clinic with anosmia and the onset of puberty. The magnetic resonance imaging revealed hypoplasia of the olfactory bulbs, and initial hormonal tests confirmed her prepubertal status, but the first genetic test was inconclusive. The girl’s pubertal development had an atypical course. After some time of observation, we performed a long luteinizing hormone-releasing hormone test which gave a pubertal response. The second genetic test revealed an FGFR1 gene mutation: the new molecular variant c.2187–2A>G,p. Estroprogestin therapy was administered with good clinical results. Early detection of Kallmann syndrome allows timely initiation of puberty-inducing treatment, resulting in normal physical and psychosocial development. Genetic confirmation of the syndrome, although rare, seems to be relevant for family planning of patients and early diagnosis in their offspring.