Sepsis is a life-threatening disease that affects millions of people every year. Rapid detection of sepsis assists clinicians to initiate timely antibiotic therapy and to reduce mortality. At the same time, accurate point-of-care detection is needed to reduce unnecessary use of antibiotics. One of the principal challenges in sepsis diagnosis is that many sepsis cases do not result in positive blood cultures. These so-called culture-negative cases present a significant health threat. In this work, we present a microfluidic cells separation system for the detection of sepsis in both culture-positive and culture-negative cases. Leukocytes were captured in several affinity separation zones of a microchip based on CD64, CD69, and CD25 expression. To validate this assay 40 septic patients and 10 healthy volunteers were enrolled in this study. Septic patients were divided into culture-positive (n = 12) and culture-negative cases (n = 21). CD64 + cell capture demonstrated excellent accuracy for sepsis detection with an area under the receiver operating characteristic curves (AUC) of 0.962. A combined panel of CD64 + and CD69 + cell counts was constructed, and the new panel outperformed each of these two biomarkers alone with the AUC of 0.978. Our affinity microfluidic devices were validated by conventional flow cytometry analysis. Results showed that the cell capture number of specific affinity region increased along with the increase of its corresponding antigen expression. This clinical validation confirms that CD64 and CD69 cell separations are a powerful sepsis assay with the potential for point-of-care analysis in culture-positive and culture-negative cases.