Courtyards are an effective passive strategy for improving the energy performance of buildings. However, there is a lack of accurate simulation tools for their thermal performance due to their complex thermodynamics. This paper's contribution is the coupling of a CFD model with a system of differential equations at the walls, governing surface and inner wall temperatures, providing an accurate computation of courtyard thermal performance. On this basis, boundary conditions for the standard Boussinesq equations governing temperatures, wind velocity, and pressure within the courtyard are established. Modelling results are compared with monitored data in two days of different months in a courtyard in Seville (Spain). Simultaneously, simulations carried out by existing software were performed. Resulting data showed more accuracy than existing tools, with a Root Mean Square Error of 1.19 (August) and 1.59 (October), while the corresponding values with ENVI-met were 3.31-3.4, and with Ladybug Tools 2.59-4.49.