The Extreme Universe Space Observatory (EUSO) is an astronomical telescope that will be hosted by the Japan Experiment Module (JEM) on the International Space Station. The telescope will determine ultrahigh-energy cosmic ray properties by measuring the UV fluorescence light generated in the interaction between the cosmic rays and the atmosphere. Therefore, cloud information is crucial for a proper interpretation of the data. To obtain the cloud top height, an infrared (IR) camera is being designed. The design is constrained by JEM-EUSO requirements, which have led to a bi-spectral camera option (10.8- and 12-μm bands). The bi-spectral design has allowed us to develop a split-window algorithm to correct the atmospheric effects and retrieve the cloud temperature from the brightness temperatures (BTs) in the bands aforementioned. The algorithm has been validated in synthetic scenarios at pixel level. The results show that the algorithm is able to retrieve the temperature with accuracy much better than the requirement of 3K. It has also been tested in two-dimensional scenarios by applying it to moderate resolution imaging spectroradiometer (MODIS) images of BTs in bands 31 similar to those of the IR camera. The retrieved temperatures are in a very good agreement with the temperatures given by MODIS.