We conducted a pilot randomized control trial (RCT) to simultaneously examine the feasibility of effectively implementing Cognitive Remediation Therapy (CRT) for adolescents with anorexia nervosa (AN) during medical hospitalization at a single-site hospital center. Employment of this protocol occurred on a general medical unit with diverse medical admitting diagnoses, not an eating disorder floor of a hospital and not part of a structured inpatient anorexia nervosa treatment program. This was the first time an RCT for a psychosocial intervention was implemented on this unit with patients with eating disorders. Here, we describe the process of piloting the study, including modifications that needed to be made to the original protocol. We also describe the feedback from major stakeholders regarding the process of conducting the pilot study. We summarize lessons learned and steps to take for smooth integration of an RCT of a therapeutic intervention on medical unit.Trial registration: ClinicalTrials.gov Identifier NCT02883413.