Ayurvedic medicine makes considerable use of Semecarpus anacardium, a tropical tree that grows wild throughout the Indian subcontinent, to treat human cancers. One of the components of the Indian Siddha medicine preparation “Kalpaamruthaa” is the nut milk extract of Semecarpus anacardium, which is said to have ulcerogenic, analgesic, antioxidant, and antipyretic properties. Because of the inhibition of angiogenic and hypoxic factors (vascular endothelial growth factor, hypoxia inducible factor-1 alpha, and inducible nitric oxide synthase characteristics), the nut extract has anticancer potential. Although its fruit has great medicinal potential, in this natural fruit setting is very less (8–16%) due to its androdioecious nature of flowering, which creates asynchronous flowering between male-biased and bisexual-biased flowers. Bisexual flowers also fail to fruit set on self-pollination. Hence, to increase the fruit set in the Semecarpus anacardium needs artificial pollination. To perform artificial pollination and long-term conservation of this important medicinal plant, cryopreservation of pollen can effectively preserve its haploid genetic diversity for an infinite period of time. This protocol aimed to long-term cryopreserve the pollen of Semecarpus anacardium for use in breeding programs in the future.