Treatment of oral pathogens is important for both oral and systemic health. The antimicrobial activity of chitosan (CS)-based scaffolds either loading antibiotics or compositing with other agents are well documented. However, the intrinsic antibacterial activity of CS scaffolds alone has never been reported. Herein, we fabricated the non-crosslinked CS scaffold and investigated its antibacterial activity against typical oral pathogens, Gram-negative Porphyromonas gingivalis and Gram-positive Streptococcus mutans. We found both pathogens were completely killed by 1 mg CS scaffolds at 6 h, due largely to the CS-induced time-dependent bacteria clustering. Interestingly, β-glycerophosphate crosslinked scaffolds showed no antibacterial activity. In conclusion, the bactericidal activity of CS scaffolds alone is reported for the first time. Together with the biodegradability, physical stability, biocompatibility and great antibacterial activity, the non-crosslinked CS scaffolds may have great potentials not only in treating oral diseases but also in wound healing and tissue engineering.