Phytochemicals and antioxidant activity of fruits of 30 B. aegyptiaca trees naturally growing in the hyper-arid and arid zones in Mauritania were evaluated by following standard procedures. Ethnobotanical uses of fruit pulps and kernel were assessed using a structured questionnaire. Balanites aegyptiaca fruit pulp is a good source of sugars (33 g/100 g dry matter (DM)), polyphenols (264 mg GAE/100 g DM) and flavonoids (34.2 mg/100 g DM) with an average antioxidant activity of 519 µmol TEAC/100 g DM. The fruit kernel is rich in lipids (46.2 g/100 g DM) and proteins (29.5 g/100 g DM). Fruits from the hyper-arid zone exhibited high level of polyphenols, antioxidant activity and soluble tannins. Almost all of the informants (97.14%) reported the use of fruit pulp in folk medicine to treat diabetes, while 72.86% reported using the fruit pulp to treat hypertension. Kernel oil is mainly employed as ointments in the treatment of paronychia (57.14%) and dermal infections (35.71%). The predominant methods for preparing/administering fruit pulp/Kernel were maceration (58.8%), sucking fruit pulp (25.7%) and decoction (24.2%). Balanites aegyptiaca fruit contain both nutritional and health-promoting phytochemicals that could be of interest in the development of strategies for sustainable use of this neglected indigenous fruit tree.