A wide range of analytical techniques have been reported to determine cordycepin (CDN) in various sample matrices. Nevertheless, greener analytical approaches for CDN estimation are scarce in the literature. As a result, this study was designed to develop and validate a stability-indicating greener “high-performance thin-layer chromatography (HPTLC)” technique for CDN determination in a laboratory-developed formulation. The greener eluent system for CDN detection was ethanol–water (75:25 v/v). At a wavelength of 262 nm, CDN was measured. The greenness scale of the proposed analytical technology was derived using the “Analytical GREENness (AGREE)” approach. The proposed stability-indicating HPTLC assay was linear for CDN analysis in the 50–1000 ng/band range with a determination coefficient of 0.9978. The proposed analytical technique for CDN analysis was simple, rapid, accurate, precise, robust, selective, stability-indicating, and greener. The AGREE score for the proposed stability-indicating HPTLC technique was calculated to be 0.79 using the AGREE calculator. The current protocol was able to detect CDN degradation products under various stress conditions, indicating its stability-indication characteristics and selectivity. The AGREE quantitative score indicated that the stability-indicating current protocol had outstanding greener characteristics. The amount of CDN in the laboratory-developed formulation was determined to be 98.84%, indicating the suitability of the current protocol in the assay of CDN in the formulations. These results suggested that CDN in a laboratory-developed formulation may be regularly determined using the stability-indicating greener HPTLC strategy.