The SARS-CoV-2 Omicron variant is more highly transmissible and causes a higher mortality rate compared to the other eleven variants despite the high vaccination rate. The Omicron variant also establishes a local infection at the extrathoracic airway level. For better health risk assessment of the infected patients, it is essential to understand the transport behavior and the toxicity of the Omicron variant droplet deposition in the extrathoracic airways, which is missing in the literature. Therefore, this study aims to develop a numerical model for the Omicron droplet transport to the extrathoracic airways and to analyze that transport behavior. The finite volume method and ANSYS Fluent 2020 R2 solver were used for the numerical simulation. The Lagrangian approach, the discrete phase model, and the species transport model were employed to simulate the Omicron droplet transport and deposition. Different breathing rates, the mouth and nose inhalation methods were employed to analyze the viral toxicity at the airway wall. The results from this study indicated that there was a 33% of pressure drop for a flow rate at 30 l/min, while there was only a 3.5% of pressure drop for a 7.5 l/min. The nose inhalation of SARS-CoV-2 Omicron droplets is significantly more harmful than through the mouth due to a high deposition rate at the extrathoracic airways and high toxicity in the nasal cavities. The findings of this study would potentially improve knowledge of the health risk assessment of Omicron-infected patients.