Phocomelia is a rare congenital condition characterized by severe limb malformation, where the limbs are either partly or completely underdeveloped. Phocomelia can occur as a syndrome or as a limb-specific abnormality. It is characterized by high rates of stillbirth, intrauterine demise, and early neonatal mortality. Administering anaesthesia to these patients is challenging because of anatomical and physiological variabilities. Limited experience exists regarding the management of this condition in surviving adults, and no standardized perioperative or anaesthetic guidelines are available. We present the perioperative management of a 22-year-old female with isolated non-syndromic phocomelia, with no history of intrauterine teratogenic exposure, who underwent anterior cervical decompression and fixation at the C3–C5 level. Key anaesthetic challenges included difficult intravenous access, complex arterial and venous catheterization due to anatomical variation, and positioning difficulties.