Mountain glacier moraine sequences and their chronologies allow us to evaluate the timing and climate conditions that underpin changes in the equilibrium line altitudes (ELAs), which can provide valuable information on the paleoclimatology of understudied regions such as tropical East Africa. However, moraine sequences are inherently discontinuous, and the precise climate conditions that they represent can be ambiguous due to the sensitivity of mountain glaciers to temperature, precipitation, and other environmental variables. Here, we used a two-dimensional (2-D) ice-flow and mass-balance model to simulate glacier extents and ELAs in the Rwenzori Mountains in East Africa over the past 31,000 yr (31 k.y.), including the Last Glacial Maximum (LGM), late glacial period, and the Holocene Epoch. We drove the glacier model with two independent, continuous temperature reconstructions to simulate possible glacier length changes through time. Model input paleoclimate values came from branched glycerol dialkyl glycerol tetraether (brGDGT) temperature reconstructions from alpine lakes on Mount Kenya for the last ~31 k.y., and precipitation reconstructions for the LGM came from various East African locations. We then compared the simulated fluctuations with the positions and ages (where known) of the Rwenzori moraines. The simulated glacier extents reached within 1.1 km of the dated LGM moraines in one valley (93% of the full LGM extent) when forced by the brGDGT temperature reconstructions (maximum cooling of 6.1 °C) and a decrease in precipitation (−10% than modern amounts). These simulations suggest that the Rwenzori glaciers required a cooling of at least 6.1 °C to reach the dated LGM moraines. Based on the model output, we predict an age of 12–11 ka for moraines located halfway between the LGM and modern glacier extents. We also predict ice-free conditions in the Rwenzori Mountains for most of the early to middle Holocene, followed by a late Holocene glacier readvance within the last 2000 yr.