The prevention, assessment, and treatment of neonatal pain and agitation continues to challenge clinicians and researchers. Substantial progress has been made in the past three decades, but numerous outstanding questions remain. In this setting, clinicians must establish safe and compassionate standardized practices that consider available efficacy data, long-term outcomes, and research gaps. Novel approaches with limited data must be carefully considered against historic standards of care with robust data suggesting limited benefit and clear adverse effects. This review summarizes available evidence while suggesting practical clinical approaches to pain assessment and avoidance, procedural analgesia, postoperative analgesia, sedation during mechanical ventilation and therapeutic hypothermia, and the issues of tolerance and withdrawal. Further research in all areas represents an urgent priority for optimal neonatal care. In the meantime, synthesis of available data offers clinicians challenging choices as they balance benefit and risk in vulnerable critically ill neonates.