Energy transduction, nutrient acquisition, and cell survival all depend on the exchange of ions across biological membranes. Ion channels are the most effective pathway to rapidly modify ion concentrations in the cells; thus, the proteins that form them are essential in all organisms. While ion channels are validated therapeutic targets in vertebrates and helminths, their potential for development of selective new drugs against protists remains mostly unexplored. In trypanosomatids, our knowledge of the mechanisms by which ion channels regulate vital functions is limited. The main constraints arise from the particular morphology and motility of the parasites that preclude us from applying direct electrophysiological methods to study transport proteins in protists. Here we describe an alternative method to express and purify ion channels from Trypanosoma cruzi, suitable for reconstitution in artificial lipidic matrices and functional electrophysiological studies.