To detect the effects of Polyporus polysaccharide (PPS), Bacillus Calmette-Guerin (BCG), and their combination on the nuclear factor kappa B (NF-kappa B) signaling pathway associated-gene expression and investigate the molecular mechanisms of the toxic-reducing effect of PPS in coordination with BCG against bladder cancer. After T739 cells were treated with PPS, BCG and their combination, the changes in mRNA and protein expression of inhibitor of kappa B kinase beta (IKK beta), NF-kappa B subunit p65 (NF-kappa B p65), intracellular adhesion molecule 1 (ICAM1) and chemokine (C-c motif) ligand 2 (CCL2) in bladder cancer cell line T739 were determined by relative quantitative real-time PCR, Western blot, and flow cytometry (FCM). NF-kappa B p65 DNA-binding activity in T739 cell was detected by biotinylated probe-ELISA, and NF-kappa B p65 nuclear expression in T739 cell was observed by immunohistochemistry. Compared with the T739 control group, the mRNA expression of IKBKB (IKK beta), Rel A (NF-kappa B p65), ICAM1 and CCL2 in T739 cells treated with BCG were increased obviously (Ratio > 2.0), as well as the expression of IKK beta, CCL2 and ICAM1 proteins. Meanwhile, NF-kappa B p65 DNA-binding activity and NF-kappa B p65 nuclear expression in T739 cells treated with BCG were up-regulated significantly (P < 0.05). Compared with the control, the increased expression in T739 cells were simultaneously down-regulated after PPS treatment, except for ICAM1 protein expression. With cells treated with a combination of BCG and PPS, the expression of genes associated with the NF-kappa B signaling pathway, such as IKBKB, ICAM1 and CCL2, were all down-regulated compared to the BCG group, as well as Rel A mRNA expression, NF-kappa B p65 DNA-binding activity and NF-kappa B p65 nuclear expression. PPS could inhibit the over-activation of the NF-kappa B signaling pathway induced by BCG in bladder cancer cells and accordingly attenuate the adverse reactions to BCG therapy.