The primary challenge in Monte Carlo dose calculations in radiotherapy is accurate modeling of the radiation device and the initial electron beam. For this purpose, this study aims to address this challenge by developing and experimentally validating a Monte Carlo model of the Elekta Synergy MLCi2 linear accelerator (LINAC) and performing a comprehensive analysis of accurate three-dimensional (3D) dose distribution calculations in radiotherapy. A detailed Monte Carlo model of the Elekta Synergy MLCi2 was developed using the EGSnrc code system (BEAMnrc/DOSXYZnrc). In particular, simulations were carried out for a 6-MV photon beam with field sizes ranging from 3 × 3 to 30 × 30 cm2. The initial beam parameters were optimized through an iterative process, specifically targeting the electron beam energy and the full-width at half-maximum. In addition, dose calculations were performed using the Source 9 implementation in DOSXYZnrc. Furthermore, all simulations were carried out on the HPC-MARWAN computing platform. Regarding the validation phase, experimental measurements were carried out using a PTW Semiflex 3D ionization chamber in a water phantom to measure and compare percentage depth doses (PDDs), lateral dose profiles, and beam quality indices. The model demonstrated excellent agreement with experimental measurements across all evaluated parameters. Specifically, PDDs showed mean errors below 0.51% and gamma index (2%/2 mm) values exceeding 97% for all field sizes. Lateral dose profiles exhibited mean errors generally below 1% with gamma passing rates approaching 100%. Furthermore, beam quality indices (TPR20,10 and D10) showed maximum deviations of 0.3% and 0.5%, respectively. The implementation of the Ihowfarless algorithm significantly improved calculation efficiency from 0.037 to 0.076. This study successfully developed and validated a Monte Carlo model for the Elekta Synergy MLCi2 LINAC for the 6-MV photon beam. Experimental measurements confirmed the model’s high accuracy, with mean errors below 1% for PDDs and lateral dose profiles, and gamma passing rates exceeding 97% for all fields studied. These results underscore the model’s reliability for independent verification of radiotherapy treatment plans.