Abstract Ice rises located in ice shelves around Antarctica act as pinning points, impeding the flow of ice in ice shelves and in the upstream ice sheet. Ice rises preserve records of past climate and associated changes in ice flow in their stratigraphy. Typically, the flow of ice in ice rises is characterized by both converging and diverging patterns, experiencing transitions from contact with bathymetric features to floating on the ocean. In this study, we develop a three‐dimensional ice flow model that is capable of simulating the internal stratigraphy of ice rises. The modeled stratigraphy can be compared with observed stratigraphy inferred from ground‐penetrating radar observations. The model simulates three‐dimensional ice flow described by the Stokes equations and evolution of ice temperature described by an advection‐diffusion equation that impacts the non‐linear ice rheology. We use our model to simulate the observed stratigraphy of Derwael Ice Rise in Dronning Maud Land, East Antarctica. Our results show a close agreement with the observed ice stratigraphy and suggest that the ice at 5% above the base is approximately 8,000 years old. Our new model enables us to relate the observed ice‐rise stratigraphy to the ice flow and its changes. Plain Language Summary Ice rises are features which form in coastal Antarctica when the ice shelf comes into contact with the ground. These features provide a force on the ice shelf and can influence the position of the grounding line. We simulate an ice rise in East Antarctica called Derwael Ice Rise, outlining the steps necessary to model the three‐dimensional layers of an ice rise and compare the modeled layers with observed layers obtained from radar measurements. Comparisons between the observed and modeled layers allow us to validate our model. Our simulations are a step forward in the calculation of ice layers in Antarctica, which will allow reconstruction of past ice‐flow patterns. Key Points We develop a three‐dimensional model to simulate the age distribution of an ice rise and the surrounding ice We compare the modeled stratigraphy of an ice rise with the stratigraphy inferred from radar observations We develop a new model initialization technique that results in simulated ice velocities closely matching observations