Peripheral blood stem cell apheresis has become a routine procedure for the collection of peripheral blood stem cells to enable high-dose chemotherapy followed by autologous stem cell transplantation in high-risk pediatric malignancies. However, the procedure remains challenging in very low-weight infants due to high extracorporeal blood volume and citrate toxicity. Our case report demonstrates in detail a successful and complication-free large-volume leukapheresis in a very small infant weighing 6 kg using a Spectra Optia apheresis system after placing a femoral double-lumen Shaldon catheter. Anticoagulation was achieved by citrate dextrose solution without the use of heparin. The total amount of blood being processed during the procedure equaled almost 4 times the total blood volume of the patient. The final apheresis product contained 14.0×10 CD34 cells/kg body weight. The infant was diagnosed with an atypical teratoid/rhabdoid tumor of the thalamus and third ventricle at the age of 3 months and had a history of epileptic seizures.