Aim To compare in vitro the sealing ability of root-end fillings with mineral trioxide aggregate (MTA) and EndoSequence BioCeramic Root Repair Material-Fast Set (BC-RRM) Putty using a novel bacterial nutrient leakage model, which provides information on whether or not intracanal bacteria are receiving nutrients from serum via leakage channels. Methodology Sixty single-rooted decoronated mandibular incisors with instrumented root canals were subjected to root-end resection and ultrasonic preparation. The root specimens were mounted in the experimental apparatus, and the root-end cavities filled with the test materials. The positive control group used warm Gutta-percha and no sealer. In the negative controls, the entire resected surface was covered with varnish. After sterilization in ethylene oxide, the root canal was inoculated with 1.5 × 105 washed cells of Enterococcus faecalis. The apparatus was filled with foetal bovine serum, leaving only the apical root immersed. After 30-day incubation, samples were taken from the canal, cultured and the colony-forming units (CFUs) counted. Statistical analysis was performed using the Mann–Whitney test for quantitative and the Fisher exact test for qualitative data. Results In the MTA group, 10 of 20 (50%) specimens still had detectable viable bacteria in the canals (mean, 8.97 × 103 CFUs). In the BC-RRM Putty group, 5 of 18 (28%) specimens were positive for bacterial growth (mean, 2.88 × 104 CFUs). There was no significant difference when comparing the quantitative or presence/absence data from the MTA and BC-RRM Putty groups. Positive and negative controls yielded the expected results. Conclusions MTA and BC-RRM Putty had similar sealing ability. The experimental model was effective in determining whether or not residual intracanal bacteria could survive by receiving nutrients from outside.