Four undescribed pyrone derivatives, pestalopyrones A-D, containing unusual tricyclic 5/6/6 polycyclic skeletons, were isolated from the ethyl acetate extract of the endophytic fungus Pestalotiopsis neglecta S3 derived from the fresh stems of Rubia podantha Diels (Rubiaceae). Their planar structures were elucidated mainly by NMR and HRESIMS. Pestalopyrones A-D contained six contiguous chiral carbons, and the relative configurations of C-4, C-5, and C-8 in tricyclic 5/6/6 polycyclic skeletons were determined by ROESY spectra. For pestalopyrone B, the absolute configuration of C-16 was determined by the Mosher's method. All isolated compounds were tested for their cytotoxicity against cancer cell lines, antibacterial activity, and inhibitory effect on the lipopolysaccharide (LPS)-induced nitric oxide (NO) production, and the results showed that pestalopyrone A inhibited LPS-induced NO production with an IC50 value of 35.8 μM.