Background Conjoined twins are an extremely rare congenital occurrence, and anesthetic management for surgical separation presents unique challenges for anesthesiologists. Case presentation Five-month-old male pygopagus conjoined twins underwent separation surgery. We performed anesthesia induction in the supine position and surgery in the prone position. This presented a challenge because the transition from supine to prone position reversed the positional relationship between the two babies, resulting in crossing of the respiratory circuits and monitors. To solve the problem, we used anesthesia machines and monitors on the opposite side of each baby during anesthesia induction. The positional relationship between the twins and anesthesia machines and monitors normalized after the change to the prone position. Following the separation surgery, the twins were discharged without any complications. Conclusions Our method of using opposite side anesthetic machines and monitors for anesthesia induction was useful for the safe anesthetic management of pygopagus conjoined twins.