Only the peel of bitter orange has proven medicinal value, mainly for digestive problems and a few other health concerns. However, in folk medicine the flower of bitter orange is also used. Folk medicine uses the flower not only to treat gastrointestinal disorders, but to treat a myriad of health problems ranging from nervousness and insomnia, to gout and sore throat, and even for obesity. In oriental medicine, the flower of the bitter orange is used for poor appetite, chest and stomach pain, and vomiting. Homeopathic practitioners use both the peel and the flower to remedy both headaches and pain.

An infusion of the fruit is thought to soothe headaches, calm palpitations, and lower fevers. The juice helps the body eliminate waste products, and, being rich in vitamin C, helps the immune system ward off infection. If taken to excess, however, its acid content can exacerbate arthritis. In Chinese herbal medicine, the unripe fruit, known as zhi shi, is thought to "regulate the qi," helping to relieve flatulence and abdominal bloating, and to open the bowels. The essential oils of bitter orange, especially neroli, are sedative.

Today bitter orange continues to be employed in a wide variety of traditions. In Latin America, the leaf of the bitter orange plant is prepared as a tonic and used as a laxative, a sedative for insomnia, and to calm anxiety. The peel of the fruit is used to treat stomach aches and high blood pressure. Some cultures use bitter orange peel as an anti-spasmodic. In traditional oriental medicine, the bitter orange peal is used for indigestion, abdominal pain, constipation, and dysenteric diarrhea. Bitter orange is still used throughout the world as a remedy for insomnia and indigestion