Negative magnetophoresis is a novel and attractive method for continuous microparticle sorting inside a magnetic medium. In this method, diamagnetic particles are sorted based on their sizes using magnetic buoyancy force and without any labeling process. Although this method provides some attractive features, such as low-cost fabrication and ease of operation, there are some obstacles that adversely affect its performance, especially for biological applications. Most types of magnetic media, such as ferrofluids, are not biocompatible, and the time-consuming process of sample preparation can be threatening to the viability of the cells within the sample. Furthermore, in this method, both the target and non-target particles are affected by the magnetic field, and therefore, a high separation efficiency cannot be achieved. In this paper, to isolate the abnormal cells from the other blood cells, a microfluidic device was designed using numerical simulation. This model utilizes negative magnetophoresis on a rotating disk, and to reduce the exposure time of the cells inside the magnetic medium, a micromixer is embedded in the upstream of the separator which rapidly prepares the sample. In this part, diluted blood sample and ferrofluid are mixed together utilizing magnetic force. Afterward, the separator sorts the cells into multiple outlets using magnetic buoyancy force as well as centrifugal force. The numerical procedure employed in this study shows that the proposed model is able to recover ∼100% of the abnormal cells from a particular outlet for binary and ternary separation of the cells with high throughputs. Although this percentage of separation may be lower in reality, the optimization of the proposed design by the numerical method can avoid trial-and-error during costly and time-consuming experiments. Also, the device proposed in this study reduces the exposure time of the cells inside the ferrofluid to just a few seconds, which can improve cell viability.