It is very rare that a foramen magnum arachnoid cyst induces compression of the spinal cord and syringomyelia, and currently there are few treatment experiences available. Here we reported the case of a 43-year-old male patient who admitted to the hospital due to weakness and numbness of all 4 limbs, with difficulty in urination and bowel movement. MRI revealed a foramen magnum arachnoid cyst with associated syringomyelia. Posterior fossa decompression and arachnoid cyst excision were performed. Decompression was fully undertaken during surgery; however, only the posterior wall of the arachnoid cyst was excised, because it was almost impossible to remove the whole arachnoid cyst due to toughness of the cyst and tight adhesion to the spinal cord. Three months after the surgery, MRI showed a reduction in the size of the arachnoid cyst but syrinx still remained. Despite this, the symptoms of the patient were obviously improved compared to before surgery. Thus, for the treatment of foramen magnum arachnoid cyst with compression of the spinal cord and syringomyelia, if the arachnoid cyst could not be completely excised, excision should be performed as much as possible with complete decompression of the posterior fossa, which could result in a satisfying outcome.