This article presents data on Coronavirus disease (COVID-19)-related learning, health, and mental health concerns of 134 families of children with heart disease (HD), the most common birth defect, who are followed by a unique hospital-based Educational Achievement Partnership Program (EAPP) designed to serve as a liaison across the family, the child's medical team, and school. At-school, remote, and hybrid learning alternatives prompted by the COVID-19 pandemic presented families with an especially complex decision to make for children with HD due to competing complications in this population: Increased susceptibility to illness, greater risk of neuropsychological problems, and higher level of individualized education services that are not readily transferable to a home learning platform. Parents of school-aged children with HD completed a survey about COVID-19-related school support needs as part of a quality improvement project. Survey results revealed 51% of children would learn from home during the 2020-2021 school year due to concerns about the child's underlying health condition, indicating a marked change in schooling modality compared to prior years (4% in 2019). Nearly 75% of families requested medical guidance for COVID-19-related school health and education plan addendums. Seventy-three percent of families had mental health concerns about their child; severity of HD was related to families' reports about mental health concerns. Findings suggest follow-up is needed by school psychologists and medical consultative collaborative partners to support the transition back to in-person schooling after the COVID-19 pandemic concludes and to identify long-term educational consequences of disrupted learning during this period.