Centrifugal counter-flow elutriation is a non-invasive technique that separates cells based on their hydrodynamic volume in a specialized centrifugation chamber that allows the application of a counter-flow of buffer to oppose sedimentation. Here, we report a centrifugal counter-flow elutriation protocol for Trypanosoma brucei cells that is able to rapidly isolate highly enriched G1 subpopulations (>95%) of synchronized cells. The cells obtained are viable and proliferate without lag, allowing subsequent cell cycle phases to be obtained by continued culture. The synchronized cell cultures obtained by this process have uniform DNA content, a narrow size distribution, undergo synchronous division, and maintain synchrony into subsequent cell cycles.