The study aimed to assess the microleakage of nanoparticle-based (NPB) cyanoacrylate sealer and epoxy resin-based (ERB) sealer using radioisotope method and confocal laser scanning microscopy (CLSM). A total of 100 single-rooted teeth were collected; specimens were accessed, instrumented, and irrigated, and randomly distributed into 4 groups of 25 samples each: Group I: Positive control, group II: Negative control, group III: Obturated with NPB sealer, and group IV: Obturated with ERB sealer. All samples were immersed in 99mTc pertechnetate solution, for 3 hours after which radioactivity was estimated under a Gamma camera. The radioactivity released by specimens before and after nail varnish removal was statistically analyzed. After 2 weeks, the same samples were used for CLSM analysis. The sealer tubular penetration depth was measured at the deepest level for each group using ZEN lite 2012. Data collected was statistically evaluated. The amount of radioactivity observed at first in group III and group IV was 194.76 and 599.12 units, respectively, with p-value < 0.001, indicating significant interaction, and after nail varnish removal, it was 89.68 and 468.44 units, respectively, with a p-value < 0.001; again, indicating statistical significance. Hence, the radioactivity of NPB sealer was found to be lower than ERB sealer in both cases, indicating better sealing of the former. The photomicrographs show that mean value of dye penetration in NPB sealer in first, second, and third segment from apex was 85.06, 75.73, and 66.09, respectively; while in the case of ERB sealer, those were 597.28, 461.17, and 195.68, respectively; with p-value < 0.001; signifying that NPB sealer exhibited higher resistance to microleakage than ERB sealer. The NPB sealer can become a potential root canal sealer in future endodontics due to superior physiochemical properties attributed to the cyanoacrylate and incorporated nanoparticles. The study clinically signifies that we can equally use the radioisotopic method along with confocal method while conducting the microleakage studies. In addition, NPB sealer can be an emerging replacement with better properties than gold standard root canal sealers for clinical use. How to cite this article: Shetty C, Qaiser S, Shetty A, et al. Evaluation of Microleakage of Nanoparticle-incorporated Cyanoacrylate Root Canal Sealer Using the Radioisotopic Method: An In Vitro Study. J Contemp Dent Pract 2024;25(4):335-341.