Phytochemical investigation of Gardenia thunbergia L. f. aerial parts led to the isolation of a previously undescribed neolignan 13, designated (thunbergiside A). This compound is classified as 2,3-dihydrobenzofuran that features a unique, highly substituted skeleton with functional diversity. The absolute configuration was established by comparing its experimental ECD spectrum and optical rotation values with those of related neolignans. In addition, seventeen diverse phytoconstituents were identified for the first time from this plant, expanding our knowledge of its chemical composition. These included oleanane-type saponins, phenolic derivatives, lignans, and neolignans, which serve as valuable chemotaxonomic markers. Considering the frequent emergence of infectious diseases, it is worth exploring additional antimicrobial agents. Selected isolated compounds were assessed for their antimycotic properties in an investigation for potential anti-infective agents. Various chromatographic procedures, spectroscopic, spectrometric analyses, and molecular modelling studies were employed for phytochemical investigation and structural characterization. Furthermore, the alamarBlue-based viability assay was employed for antifungal evaluation against three pathogenic fungi. Specifically, saponin 17, 3-O-(β-ᴅ- glucuronopyranoside) oleanolic acid, displayed moderate antifungal activity (IC₅₀ = 11 µg/mL) against Candida albicans. Overall, this study identified an unprecedented neolignan along with other diverse constituents from Gardenia thunbergia. Moreover, the study presented a potential scaffold for antifungal drug development.