Simultaneous quantification of adenosine and deoxyadenosine isomers, including 2′-deoxyadenosine (dA) and 3′-deoxyadenosine (cordycepin, COR) is a challenge because they are very similar in chemical structure. In some previous studies on food ingredients, adenine and dA might be mistakenly detected as COR that has been shown to have multiple health benefits. In this work, we developed a novel HPLC method with fluorescence detection (HPLC-FD) to simultaneously quantify COR, adenosine and dA. Pre-column derivatization with chloroacetaldehyde (CAA) was deployed. The proposed method has a limit of detection at the nM level for COR and adenosine, and is far more sensitive than the methods previously developed for COR determination. Using the present method, caterpillar fungi were analyzed as model food samples. The analysis revealed that COR was present in Cordyceps militaris and Cordyceps flowers in a concentration range from 0.314 to 0.735 mg g⁻¹, but not in Cordyceps sinensis (C. sinensis), a natural and the priciest caterpillar fungus. These results suggest that the profile of active ingredients in C. sinensis has been wrongly claimed for many years. This finding was also supported by the results from further HPLC-MS/MS analyses.