To identify the biophysical properties of blood samples consistently, macroscopic pumps have been used to maintain constant flow rates in a microfluidic comparator. In this study, the bulk-sized and expensive pump is replaced with a cheap and portable micropump. A specific reference fluid (i.e., glycerin solution [40%]) with a small volume of red blood cell (RBC) (i.e., 1% volume fraction) as fluid tracers is supplied into the microfluidic comparator. An averaged velocity (<Ur>) obtained with micro-particle image velocimetry is converted into the flow rate of reference fluid (Qr) (i.e., Qr = CQ × Ac × <Ur>, Ac: cross-sectional area, CQ = 1.156). Two control variables of the micropump (i.e., frequency: 400 Hz and volt: 150 au) are selected to guarantee a consistent flow rate (i.e., COV < 1%). Simultaneously, the blood sample is supplied into the microfluidic channel under specific flow patterns (i.e., constant, sinusoidal, and periodic on-off fashion). By monitoring the interface in the comparator as well as Qr, three biophysical properties (i.e., viscosity, junction pressure, and pressure-induced work) are obtained using analytical expressions derived with a discrete fluidic circuit model. According to the quantitative comparison results between the present method (i.e., micropump) and the previous method (i.e., syringe pump), the micropump provides consistent results when compared with the syringe pump. Thereafter, representative biophysical properties, including the RBC aggregation, are consistently obtained for specific blood samples prepared with dextran solutions ranging from 0 to 40 mg/mL. In conclusion, the present method could be considered as an effective method for quantifying the physical properties of blood samples, where the reference fluid is supplied with a cheap and portable micropump.