A two-dimensional model was developed for an axial-radial ammonia synthesis reactor of the Shiraz petrochemical plant. In this model, momentum and continuity equations as well as mass and energy balance equations are solved simultaneously by orthogonal collocation on the finite element method to obtain pressure, velocity, concentration and temperature profiles in both axial and radial directions. For the catalyst particle, the effectiveness factor is calculated by solving a two-point boundary value differential equation. The boundary conditions for the Navier-Stokes and continuity equations are obtained by using equations representing the phenomena of gases splitting or joining in different streams and going through holes in a thin wall. The results of the mathematical model have been compared with the plant data and a good agreement is obtained.