Esophageal atresia (EA) is a congenital malformation that affects the normal esophageal development. Surgical treatment, although restoring the integrity of the alimentary tract, may lead to long-term sequelae-like developmental abnormalities and musculoskeletal deformities. We evaluated the effects of osteopathic manipulative treatment (OMT) on the recovery of the range of the right upper limb movement and on the rise of the auxological parameters. A case series of five children affected by type C EA were described. Six OMT sessions were performed over a 4-month period. At each treatment, height, weight, body mass index (BMI) and range of motion (ROM) in elevation of the right upper limb were assessed. OMT was applied to improve scar, larynx, rib cage, and sternum mobility. An average change of 2.3 cm in height and an average increase of 8° in the ROM of the upper limb in the period of study were detected. Additionally, OMT could improve the anthropometric data and the mobility of the right upper limb of children surgically treated for EA. Further studies that evaluate the effectiveness of OMT in post surgical treatment of congenital malformations of the thorax can be considered in the future.