With the increasing usage of indwelling medical devices in clinical practice, the frequency of fungal infections has increased, such as that of Candida albicans (C. albicans). Biofilms, a protected niche for microorganisms, are resistant to a range of current antifungal agents. Chitosan is a polyatomic biopolymer with advantageous biocompatibility, biodegradation, nontoxicity and antibacterial properties. To investigate the inhibitory effect of chitosan on biofilms formed by C. albicans, cell viability, 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-caboxanilide reduction, and morphological assays, including fluorescence microscopy and scanning electron microscopy (SEM), were employed. As assessed by cell viability assay, chitosan showed significant inhibitory effects on the planktonic cells and the biofilm of C. albicans in a dose-dependent manner. Fluorescence microscopy and SEM assays confirmed that the chitosan-treated group showed delayed C. albicans biofilm formation with defect morphological features, due to the inhibitory effects of the vast majority of fungal cell growth. In conclusion, C. albicans biofilms were compromised by the treatment with chitosan, providing an alternative therapeutic strategy against the fungal biofilms in the medical devices.