As the pandemic wanes, there is an opportunity to reevaluate resultant changes in graduate medical education (GME), particularly from the viewpoints of those affected most. We aimed to assess both trainee and faculty perceptions on the educational changes and innovations resulting from the pandemic to inform future educational planning. We surveyed trainees and core education faculty at three New York City children's hospitals. Surveys assessed perceived changes to educational activities, skills, scholarship, effectiveness of virtual teaching, future desirability, and qualitative themes. The survey was completed by 194 participants, including 88 (45.4%) faculty and 106 (54.6%) trainees. Trainees were more likely to report a negative impact of the pandemic compared with faculty (75.5% vs. 50%, p < 0.01). Most respondents reported a decrease in formal educational activities (69.8%), inpatient (77.7%) and outpatient (77.8%) clinical teaching. Despite this, most perceived clinical and teaching skills to have stayed the same. Most (93.4%) participated in virtual education; however, only 36.5% of faculty taught virtually. Only 4.2% of faculty had extensive training in virtual teaching and 28.9% felt very comfortable teaching virtually. In the future, most (87.5%) prefer a hybrid approach, particularly virtual didactic conferences and virtual grand rounds. Faculty themes included challenges to workflows and increased empathy for trainees, while trainee themes included increased work/life balance and support, but increased burnout. Many changes and innovations resulted from the pandemic. Hospital systems and GME programs should consider this data and incorporate viewpoints from trainees and faculty when adapting educational strategies in the future. The online version contains supplementary material available at 10.1007/s40670-023-01737-8.