This case report presents a paediatric patient diagnosed with lymphocytic colitis – a histological subtype of microscopic colitis. The disease is characterised by chronic, watery, non-bloody diarrhoea, a normal endoscopic image, but abnormal histopathological findings. While this condition predominantly affects adults, there are few published cases of lymphocytic colitis in the paediatric population. A five-year-old male patient with vitiligo and nephrotic syndrome was admitted for further diagnostic evaluation of chronic diarrhoea. Remission of the diarrhoea had previously been observed during steroid therapy for nephrotic syndrome, but the symptom recurred after discontinuation of treatment. A thorough differential diagnosis was conducted. Endoscopic examination revealed no macroscopic abnormalities. Only the histopathological examination confirmed the diagnosis of lymphocytic colitis. Although the association between microscopic colitis and certain autoimmune diseases is well-established, there are no reports of coexisting vitiligo or nephrotic syndrome in a child with lymphocytic colitis.