Many microorganisms can generate pigments with different colours and structures during the growth process. In this study, an endophytic fungus producing red pigments was isolated from Cynanchum auriculatum Royle ex Wight tissue. PCR amplification sequencing was conducted, and phylogenetic analysis was performed on the ITS region sequences. Combined with morphological observation, the fungus was identified as Stemphylium lycopersici. The antioxidant activities of the pigments were evaluated in vitro and showed good antioxidant properties. Ultraviolet (UV), Raman, and Fourier transform infrared (FTIR) spectroscopy and gas chromatography-mass spectroscopy (GC-MS) were used to analyse the pigments' components, which were shown to contain phenolics and anthraquinones. Most of these components have not been previously reported in Stemphylium lycopersici, especially physcione. This study is the first report of Stemphylium lycopersici secondary metabolites and their potential use as red pigments and antioxidants. Further optimisation of the culture conditions of this fungal strain might permit its application for pigment production.