Computational models are an invaluable tool in modern biology. They provide a framework within which to summarize existing knowledge, enable competing hypotheses to be compared qualitatively and quantitatively, and to facilitate the interpretation of complex data. Moreover, models allow questions to be investigated that are difficult to approach experimentally. Theories can be tested in context, identifying the gaps in our understanding and potentially leading to new hypotheses. Models can be developed on a variety of scales and with different levels of mechanistic detail, depending on the available data, the biological questions of interest, and the available mathematical and computational tools. The goal of this review is to provide a broad picture of how modeling has been applied to reproductive biology. Specifically, we look at four uses of modeling: (i) comparing hypotheses; (ii) interpreting data; (iii) exploring experimentally challenging questions; and (iv) hypothesis evaluation and generation. We present examples of each of these applications in reproductive biology, drawing from a range of organisms—including Drosophila, Caenorhabditis elegans, mouse, and humans. We aim to describe the data and techniques used to construct each model, and to highlight the benefits of modeling to the field, as complementary to experimental work.