Courtyards are a passive strategy to improve the energy performance of buildings. However, the accurate simulation of courtyards’ thermodynamic performance in the early design stage is still challenging, even though there has been an emergence of new methods to assess outdoor simulation. This paper tests a novel workflow using the Ladybug Tools that uses CFD for outdoor temperature and comfort simulation of courtyards and is suitable for the early stage of building design, comparing the results with monitored data and simulated data from ENVI-met. Results show high accuracy in the prediction of temperature from Ladybug Tools with error ranges from 3.8–7.5%, which is lower than with ENVI-met. In terms of comfort, the simulated Universal Thermal Climate Index values differ by up to 10°C between ENVI-met and the Ladybug Tools. The results show a significant improvement towards the design of the courtyard in the search for net-zero energy buildings.