Background The role of polysaccharides isolated from the Ganoderma species of fungi in innate immunity has recently become a topic of research. Although some work has been conducted concerning Ganoderma lucidum, the characteristics of polysaccharides isolated from Ganoderma neojaponicum (Imazeki) as immunomodulatory agents are largely unknown. The aims for this study were to isolate and characterize the intracellular polysaccharides (IPSs) and extracellular polysaccharides (EPSs) of G. neojaponicum from STR reactor. Results The production of EPS and IPS was optimized on day 4 of the cultivation time in 2 L STR reactor based on the amount of biomass yield, total carbohydrate, β-glucan and a-glucan content. Further analysis, both the EPSs and IPSs showed the enhancement on proliferation and increment of phagocytosis activities of macrophage (RAW264.7) cell lines. Using an oral toxicity test, we also observed that 2000 mg/kg body weight/day dosage of dried G. neojaponicum mycelium does not cause any significant toxic effects on Sprague-Dawley rats in 14 d of administration. Conclusion The findings of this study indicate that the IPSs and EPSs of G. neojaponicum have the potential to be used as immunomodulating agents to stimulate the innate immune system for fighting infectious diseases. The polysaccharides from G. neojaponicum have to be further commercially explored as an alternative for medicinal Ganoderma variety of G. lucidum production.