Paper-based microfluidic devices have many applications in biomedical and environmental analysis. However, the process of prototyping device designs can be tedious, error-prone, and time-consuming. Here, we present a cross-platform, open-source software tool-AutoPAD-developed to quickly create and modify device designs and provide a free alternative to commercial design software. The capabilities that we designed to be inherent to AutoPAD (e.g., automatic zone alignment and design refactoring) highlight its potential use in nearly any paper-based microfluidic device application and for creating nearly any desired design, which we demonstrate through the recreation of numerous device designs from the literature.