Achalasia is a rare primary oesophageal motility disorder that presents as a functional obstruction at the oesophago-gastric junction. The prevalence of achalasia in Down syndrome is much higher, which implies a unique association between these two uncommon conditions. Although the exact aetiology of achalasia is unknown, studies have proposed that its pathogenesis is related to autoimmune, infectious or genetic factors, leading to the intrinsic loss of inhibitory myenteric neurons in both the oesophagus and lower oesophageal sphincter. We herein report the case of a 16-month-old girl with Down syndrome and achalasia who was initially treated for gastro-oesophageal reflux disease. The diagnosis of achalasia was made only when her condition deteriorated, with subsequent failure to thrive, and upon further investigations, including barium swallow study and upper endoscopy. We also review the various mechanisms postulated in the development of achalasia in Down syndrome, as well as the various treatment modalities available for this rare disorder.