A pilot mindfulness home intervention was conducted for 6 weeks among 8–12-year-old children born with esophageal atresia and their parents. Participants were randomly assigned to a waiting list control (WLC) group (n = 8) and an experimental group (n = 12). When all participants had completed the mindfulness-based program, data were pooled and treated for the entire sample (n = 19). Selfassessment measures included the Mindful Attention Awareness Scale for Adolescents (MAAS-A), the Child and Adolescent Mindfulness Measure CAMM), the modified Spielberger State-Trait Anxiety Inventory—Child (STAIC), the Children’s Depression Inventory (CDI), and the Cognitive Emotion Regulation Questionnaire Kids version (CERQ-k). Parental assessment measures included the modified STAI-C. The results underlined the program’s feasibility and acceptability. Clinical effects of the mindfulness-based program were observed. Self-assessed data for children who had practiced mindfulness compared to the WLC group showed increased mindfulness and decreased depression. Reduced anxiety was found in all groups. Positive affect tended to improve from pre-test to post-test in children who had practiced mindfulness compared to the WLC group. Parental assessments showed significant improvement in positive affect and decreases in anxiety and negative affect in the intervention group compared to the WLC group. Cognitive emotion regulation strategies were also affected by the mindfulness-based program. Rumination scores significantly decreased from pre-test to post-test in the intervention group. This preliminary study suggests that regular mindfulness practice presents a promising approach to reducing the burden of this neonatal malformation.