For children with severe physical and cognitive disabilities (e.g. iatrogenic neurologic injury, congenital myelopathy, or quadriplegic cerebral palsy), there are limited therapeutic options. Scientific and clinical developments in implantable brain-computer interface (BCI) technology are in clinical trials in adults. The ethical issues around implantable BCI research in adults have recently been examined, but to date, only limited literature is available on the ethical issues that are attendant with implantable pediatric BCI research. Here, we summarize the ethical issues, focusing on (1) whether invasive BCI research should proceed in children, (2) regulatory considerations, (3) study design considerations, (4) pediatric recipient selection for invasive BCI trials, (5) special problems regarding informed consent in this context, and (6) related psychosocial and public perception considerations. We conclude with specific recommendations regarding ethically informed design of invasive pediatric BCI trials.