Dysphagia and vocal cord dysfunction are frequent complications after congenital heart surgery. Both are risk factors for aspiration, which can lead to pneumonia, progressive lung disease, and respiratory arrest. A protocol was implemented to promote early detection of aspiration in a high-risk cohort of patients. Retrospective data were collected on all patients under 120 days old who underwent the Norwood procedure, aortic arch repair, Blalock–Taussig shunt placement, or cervical cannulation for extracorporeal membrane oxygenation from 10/2012 to 05/2016 at a single institution. Patients underwent an assessment of symptoms, fiberoptic endoscopic evaluation of swallowing (FEES), and modified barium swallow (MBS) study in the postoperative period prior to initiating oral feeds. Patients with and without aspiration were compared. Of the 96 patients included in the study, one-third (33%) of patients had evidence of vocal cord dysfunction by FEES and just over half (51%) had evidence of aspiration by FEES or MBS. Most (73%) of the patients with aspiration were asymptomatic and a majority (53%) of patients with aspiration had normal vocal cord function. Aspiration is common after congenital heart surgery, and an assessment of vocal cord or swallow function in isolation may lead to underdiagnosis. A comprehensive protocol including MBS and FEES is necessary for the early detection of vocal cord dysfunction and aspiration and may prevent adverse outcomes in high-risk postoperative patients.