The effect of ferrous sulfate addition on production of cordycepin (3′-deoxyadenosine), a useful bioactive product with some pharmacological activities, was investigated in submerged cultures of Cordyceps militaris in shake flasks. The results showed that the optimal addition condition was on day 0 with 1 g/L of ferrous sulfate, and the maximal amount of cordycepin reached 596.59 ± 85.5 mg/L, about 70% higher than the control without ferrous sulfate addition. Meanwhile, the consumption of inosine 5′-monophosphate (IMP), a potential precursor of cordycepin, was decreased rapidly. Transcription levels of important genes encoding adenylosuccinate synthetase ( purA), IMP cyclohydrolase ( purH) and IMP dehydrogenase ( guaB) in the purine nucleotide biosynthetic pathway were also studied. Compared to the control, the transcription level of purA was significantly up-regulated in ferrous sulfate supplemented cultures, while purH and guaB were slightly down-regulated. This work indicated that ferrous sulfate addition was a simple and useful strategy for improving cordycepin production, and the related information might be helpful for further manipulation and understanding of the cordycepin biosynthesis.