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(1) Background: Few antifungal drugs are currently available, and drug-resistant strains have rapidly emerged. Thus, the aim of this study is to evaluate the effectiveness of the antifungal activity from a combinational treatment of chitosan with a clinical antifungal drug on <i>Candida albicans</i> and <i>Candida tropicalis</i>. (2) Methods: Minimum inhibitory concentration (MIC) tests, checkerboard assays, and disc assays were employed to determine the inhibitory effect of chitosan with or without other antifungal drugs on <i>C. albicans</i> and <i>C. tropicalis</i>. (3) Results: Treatment with chitosan in combination with fluconazole showed a great synergistic fungicidal effect against <i>C. albicans</i> and <i>C. tropicalis</i>, but an indifferent effect on antifungal activity when challenged with chitosan-amphotericin B or chitosan-caspofungin simultaneously. Furthermore, the combination of chitosan and fluconazole was effective against drug-resistant strains. (4) Conclusions: These findings provide strong evidence that chitosan in combination with fluconazole is a promising therapy against two <i>Candida</i> species and its drug-resistant strains.