We present BackboneLearn: an open-source software package and framework for scaling mixed-integer optimization (MIO) problems with indicator variables to high-dimensional problems. This optimization paradigm can naturally be used to formulate fundamental problems in interpretable supervised learning (e.g., sparse regression and decision trees), in unsupervised learning (e.g., clustering), and beyond; BackboneLearn solves the aforementioned problems faster than exact methods and with higher accuracy than commonly used heuristics. The package is built in Python and is user-friendly and easily extensible: users can directly implement a backbone algorithm for their MIO problem at hand. The source code of BackboneLearn is available on GitHub (link: https://github.com/chziakas/backbone_learn).