Horseshoe kidneys (HSK) are the most prevalent congenital renal fusion anomalies. Its atypical anatomy with a high prevalence of vascular anomalies makes the HSK a challenging target for partial nephrectomy. Various preventive measures are to be considered before engaging in this particular surgery. In this case report, we outline our cautious surgical approach for a case of partial nephrectomy, which included an isthmectomy for safe tumour resection.