Pygopagus twin is a rare congenital malformation with a worldwide incidence of 1in 200,000. Few literature reports are published regarding the matter. In some cases, neuromonitoring is essential for safe surgical separation. We believe it is important to share our challenges and nuances in order to minimize obstacles one might encounter. We utilized neuromonitoring during our separation of both twins, and we planned a multidisciplinary approach and efficient communication system with the other teams in order to plan a successful, safe, and timely separation of the twins. We seek to highlight not our success but rather the obstacles and challenges we encountered during the separation of pygopagus twins in our institute using neuromonitoring for future reference.