The prognosis or effects of the disease also depends on the underlying causes. If Primary Amenorrhea has resulted from a structural or numerical abnormality of the chromosomes, the disease cannot be treated. Managing the symptoms through available methods may be resorted to.

If hormonal imbalance is the causative factor, then the condition may be corrected by the appropriate treatments like administration of hormones.

Primary Amenorrhea, if caused by a tumor, like that in the pituitary gland, may be corrected by surgically removing the growth.