Deoxyaconitine is primarily known for its presence in certain toxic plants, especially in the genus Aconitum, commonly referred to as monkshood or wolfsbane. Its main application lies in traditional medicine, where it has been used in highly controlled and processed forms for analgesic and anti-inflammatory purposes. In some traditional systems, it is employed to treat chronic pain, rheumatic conditions, and neuralgia. However, due to its high toxicity and narrow therapeutic window, its use is extremely limited and requires expert preparation to reduce harmful effects.

In modern pharmacology, deoxyaconitine serves as a research tool for studying sodium channel function in nerve and muscle cells, as it modulates voltage-gated sodium channels, affecting neuronal excitability. This property makes it valuable in neuroscience for understanding ion channel behavior and neurotoxicity mechanisms. Despite its biological activity, it is not used in mainstream medicine due to safety concerns.