Craniopharyngioma is uncommon benign intracranial tumour that can be cured by surgical resection followed by conventional radiotherapy. However, its anatomical localisation makes the treatment hazardous or impossible. This case report aims to discuss the first local experience of using beta-emitting Yttrium-90 radioisotope in treating a patient with refractory cystic craniopharyngioma. A 43-year-old male who has underlying refractory cystic craniopharyngioma complicated with visual impairment and panhypopituitarism was referred to our nuclear medicine department for intra-cavitary irradiation therapy. Initially, he was presented with blurring of vision and headache which he had two previous resection surgeries of cystic craniopharyngioma. However, due to persistent symptoms, he had Ommaya reservoir shunt inserted for regular aspiration. Despite regular aspiration, his symptoms worsen. He was unsuitable for radiotherapy thus was considered for intra-cystic irradiation with radioisotope. Prior to the therapy, he had pre-therapy assessment with Tc-99 m MAA. He subsequently received Ytrrium-90 citrate colloid of 300 Gy radiation dose to the inner surface of the tumour which complicated with post therapy inflammatory reaction. This first local experience highlights the role of radioisotope as the valuable minimally invasive adjuvant therapy in treating a patient with refractory cystic craniopharyngioma. Further follow-up is necessary to assess the outcome and possible late complications.