In transfusion medicine, the deformability of stored red blood cells (RBCs) changes during storage in blood banks. Compromised RBC deformability can reduce the transfusion efficiency or intensify transfusion complications, such as sepsis. This paper reports the microfluidic mechanical measurement of stored RBCs under the physiological deformation mode (that is, folding). Instead of using phenomenological metrics of deformation or elongation indices (DI or EI), the effective stiffness of RBCs, a flow velocityindependent parameter, is defined and used for the first time to evaluate the mechanical degradation of RBCs during storage. Fresh RBCs and RBCs stored up to 6 weeks (42 days) in the blood bank were measured, revealing that the effective stiffness of RBCs increases over the storage process. RBCs stored for 1 week started to show significantly higher stiffness than fresh RBCs, and stored RBC stiffness degraded faster during the last 3 weeks than during the first 3 weeks. Furthermore, the results indicate that the time points of the effective stiffness increase coincide well with the degradation patterns of S-nitrosothiols (SNO) and adenosine triphosphate (ATP) in RBC storage lesions.