Assessing motor cortical excitability (CE) is essential in transcranial magnetic stimulation (TMS) in order to ensure both safe and normalised stimulation power across subjects or patients. However, there is still a lack of automatic and easy-to-use tools for analysing the electromyographic (EMG) signal features that are relevant for CE assessment, such as the amplitude of motor evoked potentials (MEPs) or the duration of cortical silent periods (CSPs). Here, we describe CortExTool, a signal processing toolbox we developed to fulfil these needs. The toolbox, developed in the Matlab programming language, is open-source and freely accessible to the TMS community. CortExTool provides all the standard functionalities required to automatically process EMG signals recorded during a CE experiment, on both individual and group levels. Its use should allow to standardize and to facilitate the processing of CE measurements by TMS.