Background <p><i>Cordyceps militaris</i> (Cordycipitaceae) is a parasitic fungus that infects insects or larvae hosts and has been widely used to boost energy and enhance the immune system. A well-known nucleoside from <i>C. militaris</i>, cordycepin (3′-deoxyadenosine), has been reported to exhibit anti-inflammatory, anti-microbial, and anti-oxidant activities.</p> Methods <p>In this study, nine compounds were isolated from <i>C. militaris</i> using chromatographic purification techniques, and their structures were elucidated using spectroscopic analyses, including UV and NMR.</p> Results <p>Four tryptophan-containing cyclic dipeptides (<b>1</b>–<b>4</b>) were isolated from this species for the first time along with five known compounds, and the separation techniques for diketopiperazines were explained. The skeleton of the compounds <b>1</b>–<b>4</b> is reported for the first time from this species.</p> Conclusion <p>By expanding the chemical profile of <i>C. militaris</i>, our results may open new avenues for investigating its various biological potentials.</p> Graphical abstract <p></p>