Chagas disease affects around 6–8 million people worldwide. The available treatments have considerable limitations, including their uncertain efficacy in the chronic phase of the disease in adults, their unfavorable safety profile that usually compromises adherence to treatment, their long duration, and the emergence of resistant strains. All these considerations justify the continuous search for improved therapies. Informatics has been increasingly integrated into all levels of biomedical sciences, including the discovery and development of new drugs. In silico methods are relevant in all domains of therapeutics, but especially in the field of neglected diseases, in which their adoption can leverage the active participation of low- and middle-income countries (the ones historically affected by these diseases) in the development of new diagnostic and therapeutic options. This chapter describes the in silico methodologies that can be used to validate new pharmacological targets, compile data sets to train and/or validate computational models to apply in in silico screening campaigns, and implement retrospective and prospective in silico screening experiments.