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Persistent infections have become a challenge in dentistry because of growing antibiotic resistance. Nonsteroidal anti-inflammatory drugs (NSAIDs) appear to be a therapeutic alternative to control biofilm infection. The objective of this work is to evaluate the antimicrobial activity and cytotoxicity of sodium diclofenac (DCS), ibuprofen (IBP) and ibuprofen arginine (IBP-arginine) solutions against endodontic polymicrobial biofilms. Sterile radicular dentin blocks of 4 mm × 4 mm × 0.7 mm were used as substrate to grow biofilm. The dentin blocks were submerged into solutions for 5 min. The antimicrobial activity was evaluated by means of the adenosine triphosphate (ATP) assay and confocal laser scanning microscopy (CLSM). Fibroblasts 3T3-L1 (ECACC 86052701) were used to test the cytotoxicity of irrigating solutions. The antibiofilm effects determined by the ATP assay showed that 4% IBP-arginine solution exerted the highest antibiofilm activity, followed by 4% DCS and 4% IBP, with statistical differences among groups (p < 0.001). As for CLSM, 4% DCS and 4% IBP-arginine solutions gave the lowest viable cell percentages, without significant differences between them. Cytotoxicity results at 1/10 dilution were similar for all solutions. At 1/100 dilution, a 4% DCS solution obtained the lowest cell viability for both time periods assayed, 1 h and 24 h. The IBP-arginine group showed the highest cell viability at 24 h. In this preliminary study, in terms of antibiofilm activity and cytotoxicity, a mixed 4% IBP-arginine solution gave the most promising results. NSAID solutions could be recommendable drugs for endodontic disinfection procedures.