Little is known about the prevalence, characterization and treatment of pain in children with progressive neurologic, metabolic or chromosomal conditions with impairment of the central nervous system. The primary aims of this study were to explore the differences between parental and clinical pain reporting in children with life-limiting conditions at the time of enrollment into an observational, longitudinal study and to determine if differences in pain experiences were associated with patient- or treatment-related factors. Pain was common, under-recognized and undertreated among the 270 children who enrolled into the “Charting the Territory” study. Children identified by their parents as experiencing pain (n=149, 55%) were older, had more comorbidities such as dyspnea/feeding difficulties, were less mobile with lower functional skills and used analgesic medications more often, compared to pain-free children. Forty-one percent of children with parent-reported pain (21.8% of all patients) experienced pain most of the time. The majority of clinicians (60%) did not document pain assessment or analgesic treatment in the medical records of patients who were experiencing pain. Documentation of pain in the medical record was positively correlated with children receiving palliative care services and being prescribed analgesics, such as acetaminophen, nonsteroidal anti-inflammatory drugs and opioids, as well as the adjuvant analgesics gabapentin and amitriptyline.