Cordyceps sinensis (CS) is an herbal tonic in traditional Chinese medicine and is used to treat a wide range of disorders, including immune, kidney, respiratory, lung and cardiovascular diseases, in China. Most studies are focused mainly on nucleotides and polysaccharides from CS and consider them to be the main active ingredients, while other ingredients are often disregarded. Hundreds of sphingolipids have been identified from CS and showed inhibitory effects on mouse splenic lymphocytes. This study aimed to establish a method for preparing a fraction of sphingolipids from the mycelial powder of CS and evaluate its immunosuppressive activity. Fraction of sphingolipids (Fr-SPLs) were prepared by silica gel chromatography and reversed-phase chromatography. Its components were identified and quantified by Quadrupole-Orbitrap UHPLC–MS/MS. PBMCs were prepared from human blood, and splenic lymphocytes, B cells, and T cells were prepared from mouse spleens. The inhibitory effect of Fr-SPLs on cell viability was evaluated by CCK-8 assay. PBMC apoptosis and the ratio of CD4+ T cells and CD8+ T cells were quantified by flow cytometry analysis. The expression of IL-2, IL-10, and TNF-α in PBMCs was detected by ELISA kits. A fraction containing 84.83% of sphingolipids (SPLs) was prepared from the mycelia of CS and named Fr-SPLs. 15 SPLs were identified from the Fr-SPLs. Fr-SPLs significantly inhibited the viability of human peripheral blood mononuclear cells (PBMCs) with an IC50 value of 9.82 μg/mL and promoted PBMC apoptosis in a dose-dependent manner. Moreover, Fr-SPLs inhibited the viability of mouse splenocytes, as well as that of B cells and T cells derived from splenocytes. Furthermore, Fr-SPLs reduced the production of IL-2, IL-10, and TNF-α in PBMCs. Fr-SPLs show immunosuppressive activity, and this study will be useful for preparing immunosuppressive components from CS and its mycelia for hyperimmune disease. Display omitted 1.A fraction containing 15 sphingolipids (SPLs) with a content of 84.83% is prepared from the mycelia of Cordyceps Sinensis and named Fr-SPLs.2.The wild Cordyceps Sinensis contains these 15 sphingolipids.3.The Fr-SPLs exhibits an immunosuppressive activity.4.The Fr-SPLs has the potential to alleviate the symptoms caused by the COVID-19