Circulating tumor cells (CTCs) are highly correlated with the invasive behavior of cancer; as such, the ability to isolate and quantify CTCs is of great biomedical importance. This research presents a multi-stage multi-orifice flow fractionation (MS-MOFF) device formed by combining three single-stage multi-orifice segments designed for separating breast cancer cells from blood. The structure and dimensions of the MS-MOFF were determined by hydrodynamic principles to have consistent Reynolds numbers (Re) at each multi-orifice segment. From this device, we achieved improved separation efficiency by collecting and re-separating non-selected target cells in comparison with the single-stage multi-orifice flow fractionation (SS-MOFF). The recovery of breast cancer cells increased from 88.8% to greater than 98.9% through the multi-stage multi-orifice segments. This device can be utilized to isolate rare cells from human blood, such as CTCs, in a label-free manner solely through the use of hydrodynamic forces.