Assessment and management of pain for pediatric patients receiving stem cell transplants can be challenging for a health care team. Diagnostic evaluation and interventions vary between institutions and individual provider practices. In this review, we investigate and describe approaches to pain management for the most common sources of pain in pediatric patients undergoing stem cell transplants. Mucositis pain, abdominal pain, and hemorrhagic cystitis emerged as the most frequent sources of acute pain in children during conditioning and transplantation periods. Furthermore, psychosocial distress and psychological pain or distress constitute significant components of the total pain experienced by children undergoing stem cell transplantation. We will expand upon appropriate usage and escalation of opioids, as well as complementary interventions and timely initiation of interventions, in order to help control pain in these clinical syndromes.