Introduction and importance: Fanconi syndrome affects kidney function, whereas hypogonadotropic hypogonadism (HH) is gonadal failure due to deficient hormones. Diagnosis involves assays and imaging, whereas treatment targets cause and fluid balance. Here, there is a reported co-occurrence in Pakistan. Case presentation: A 14-year-old girl presented with joint pain and developmental delay. Physical examination revealed wrist widening, genu-varum, and underdeveloped secondary sexual characteristics. Laboratory findings confirmed Fanconi syndrome and coincidental ultrasound findings revealed HH. The patient received treatment in the form of oral medications and supplements to manage the condition. Clinical discussion: Fanconi syndrome is a complex disorder affecting the proximal tubule of the kidneys, leading to impaired reabsorption of various substances. In this case, potential genetic and acquired causes were ruled out, including inborn errors of metabolism and heavy metal intoxication. Prolonged valproic acid use was also considered but not confirmed as the cause. The patient also presented with HH, which is unrelated but coexisting. Treatment for Fanconi syndrome focuses on correcting electrolyte imbalances, whereas hormone replacement therapy is considered for HH. The patient’s progress and response to treatment are under careful monitoring. Conclusion: This case highlights the need for further research and comprehensive diagnostic evaluation to better understand the association between Fanconi syndrome and HH, emphasizing the importance of early diagnosis and management to prevent long-term complications.