Traditional medicine of Bhutan was once the primary provider of health care services in Bhutan and continues to deliver services to the Bhutanese population as part of the integrated medical system. This chapter reviewed the phytochemicals present in the high-altitude medicinal plants of Bhutan isolated through natural products isolation studies and the pharmacological properties of the extracts and phytochemicals. Phytochemicals were isolated from 11 medicinal plants, and these represent less than 2% of medicinal plants known in Bhutan. More than 50 metabolites were isolated belonging to alkaloids, flavonoids, terpenes, phenylpropanoids, and furanocoumarins. Primarily, diterpenoid alkaloids were isolated from two Acotinium species, whereas isoquinoline alkaloids were obtained from Meconopsis simplicifolia and three Corydalis species. Anthocyanins and flavonol glycosides were isolated as constituents of blue and yellow flowers of four Meconopsis species that feature in BTM. The crude extracts and selected isolated metabolites from medicinal plants A. laciniatum, A. nubigena, C. bhutanica, C. crispa, C. dubia, M. simplicifolia and H. amabile reportedly exhibited anti-inflammatory and immunomodulatory activities, as well as antiplasmodial properties. These reported pharmacological properties were consistent with the traditional uses and validate their uses in BTM.