Botulinum toxin A (BT-A), a potential neurotoxin produced by the bacterium Clostridium botulinum, is known for its ability to prevent the release of acetylcholine at the neuromuscular synapse, leading to temporary muscle paralysis. BT-A is used for a wide range of therapeutic applications. Several studies have shown mechanisms beyond the inhibition of acetylcholine release for pain control. BT-A inhibits the release of neurotransmitters associated with pain and inflammation, such as glutamate, CGRP, and substance P. Additionally, it would be effective in nerve entrapment leading to neuronal hypersensitivity, which is known as a new pathogenesis of painful conditions. BT-A has been applied to the treatment of a wide variety of neurological disorders. Since 2010, BT-A application has been approved and widely used as a chronic migraine prophylaxis. Moreover, due to its effects on pain through sensory modulation, it may also be effective for other headaches. Several studies using BT-A, at different doses and administration sites for headaches, have shown beneficial effects on frequency and severity. In this review, we provide an overview of using BT-A to treat primary and secondary headache disorders.