Cordycepin, also known as 3'-deoxyadenosine, is a bioactive natural antibiotic with numerous pharmacological properties including anticancer activity. Unfortunately, cordycepin is rapidly deaminated by adenosine deaminase (ADA) in vivo, which leads to the inactivation of this potent natural compound. In the present study, an ADA-resistant cordycepin prodrug (2) with the 6-NH2 masked by a glutamate-based protecting group was developed. Additionally, this cordycepin prodrug exhibited stability in serum-containing media. The prodrug is non-toxic in its standalone form, and the release of cordycepin occurs in the presence of Pseudomonas carboxypeptidase G2 (CPG2), rendering it appropriate for directed enzyme prodrug therapy. The concurrent application of CPG2 and prodrug significantly reduced the proliferation of 4T1 and U251 cancer cells, promoted apoptosis, and impeded the colony formation of 4T1 cells. Subsequent assessments utilizing the patient-derived breast cancer organoid model have demonstrated notable anticancer efficacy. The development of this prodrug presents a promising strategy to mitigate the inactivation of cordycepin in cancer therapy and minimizing toxicity to healthy cells.