The pharmacological values of Cordyceps spp. are substantially associated with the existence of an extremely potent biometabolite: cordycepin. This component exhibits powerful therapeutic activity against cancer, diabetes, and hyperlipidemia and acts as a strong immunomodulator. Extensive pharmaceutical exploitation of Cordyceps spp. has depleted its natural existence. Therefore, there is a strong need for metabolic engineering-based approaches that could be employed for overproduction of the desired metabolite, which would sustain market demands. Replacement of the old conventional genome editing tools by the newly developed CRISPR technology is considered a suitable alternative for enhancing metabolite production. Another novel approach, POPCORN, optimizes carbon/nitrogen ratios to design synthetic media for Cordyceps production. In fact, the addition of FeSO4 and porcine liver extract and alterations in the dissolved oxygen enhanced cordycepin production in the submerged state. Ultraviolet mutagenesis is another approach for the augmentation of this pharmaceutically potent biometabolite. Therefore, the main objective of this review is to present the outlook on pharmaceutical properties of cordycepin along with the metabolic approaches for enhancing cordycepin production.