Inonotus obliquus mushroom, which is a fungus belonging to Hymenochaetaceae family, is known to grow on birth trees in colder northern climates and to be a fungal parasite that draws nutrients out of living trees rather than from the ground. For the separation of protein-bound polysaccharide (PBP) from the culture broth and mycelium of Inonotus obliquus, three well known extraction methods namely hot water, ultrasound and microwave were used. The best extraction conditions to separate the PBP (64.94 mg/g) from mycelium by microwave were found to be for 1 hour and $150^{circ}C$. The possibility for concentration of extracted PBP solution by using membrane was also studied. The extracted PBP solution was concentrated effectively by using an ultrafiltration membrane and the molecular weight cut off (MWCO) is 30 KDa. It was observed that a concentration by the ultrafiltration membrane is essential not only for the development of clean separation technology but also for enhanced production of PBP. As a result, we have shown that PBP in the final concentrated solution showed approximately 10 times higher than that in the crude solution by application of the developed separation systems. The separation yield of PBP was about 89.79% by gel filtration of purification steps and the purified product was confirmed to be PBP by using FT-IR.