Biofilm communities are tolerant to antimicrobials and difficult to eradicate. This study aimed to investigate the effect of melittin, an antimicrobial peptide, either alone or in combination with deoxyribonuclease (DNase), an inhibitor of extracellular deoxyribonucleic acid (eDNA), against Enterococcus faecalis (E. faecalis) biofilms, and biofilm susceptibility to sodium hypochlorite (NaOCl). Biofilms of E. faecalis were developed in root canals of bovine teeth. The biofilms were treated with distilled water (control), melittin, DNase, or DNase+melittin. The antibiofilm effects of the treatments were analyzed using colony forming unit (CFU) assay, crystal violet staining, confocal laser scanning microscopy (CLSM), and field emission scanning electron microscope (FE-SEM). The susceptibility of DNase+melittin-treated biofilms to NaOCl (0%, 2.5% and 5%) was investigated by the CFU assay. The data were statistically analyzed using one-way analysis of variance, followed by Tukey’s test. A p-value of <0.05 was considered significant. Specimens treated with DNase+melittin showed a more significant decrease in the CFUs, eDNA level, and biofilm formation rate than those treated only with melittin or DNase (p < 0.05). CLSM analysis showed DNase+melittin treatment significantly reduced the volume of biofilms and extracellular polymeric substance compared to either treatment alone (p < 0.05). FE-SEM images showed a high degree of biofilm disruption in specimens that received DNase+melittin. 2.5% NaOCl in specimens pretreated with DNase+melittin showed higher antibacterial activity than those treated only with 5% NaOCl (p < 0.05). This study highlighted that DNase improved the antibiofilm effects of melittin. Moreover, DNase+melittin treatment increased the susceptibility of biofilms to NaOCl. Thus, the complex could be a clinical strategy for safer use of NaOCl by reducing the concentration.