Background: Online Monte Carlo (MC) treatment planning is very crucial to increase the precision of intraoperative radiotherapy (IORT). However, the performance of MC methods depends on the geometries and energies used for the problem under study. Objective: This study aimed to compare the performance of MC N-PARTICLE Transport Code version 4c (MCNP4c) and Electron Gamma Shower, National Research Council/easy PARTICLE PROPAGATION (EGSnrc/Epp) MC codes using similar geometry of an INTRABEAM® system. Material and Methods: This simulation study was done by increasing the number of PARTICLEs and compared the performance of MCNP4c and EGSnrc/Epp simulations using an INTRABEAM® system with 1. 5 and 5 cm diameter spherical applicators. A comparison of these two codes was done using simulation time, statistical uncertainty, and relative depth-dose values obtained after doing the simulation by each MC code. Results: The statistical uncertainties for the MCNP4c and EGSnrc/Epp MC codes were below 2% and 0. 5%, respectively. 1e9 PARTICLEs were simulated in 117. 89 hours using MCNP4c but a much greater number of PARTICLEs (5e10 PARTICLEs) were simulated in a shorter time of 90. 26 hours using EGSnrc/Epp MC code. No significant deviations were found in the calculated relative depth-dose values for both in the presence and absence of an air gap between MCNP4c and EGSnrc/Epp MC codes. Nevertheless, the EGSnrc/ Epp MC code was found to be speedier and more efficient to achieve accurate statistical precision than MCNP4c. Conclusion: Therefore, in all comparisons criteria used, EGSnrc/Epp MC code is much better than MCNP4c MC code for simulating an INTRABEAM® system.