In this study, we demonstrate that phase-resolved Doppler optical frequency domain imaging (OFDI) is very suitable to quantify the pulsatile blood flow within a vasodynamic measurement in the in vivo mouse model. For this, an OFDI-system with a read-out rate of 20 kHz and a center wavelength of 1320 nm has been used to image the time-resolved murine blood flow in 300 μm vessels. Because OFDI is less sensitive to fringe washout due to axial sample motion, it is applied to analyze the blood flow velocities and the vascular dynamics in six-week-old C57BL/6 mice compared to one of the LDLR knockout strain kept under sedentary conditions or with access to voluntary wheel running. We have shown that the systolic as well as the diastolic phase of the pulsatile arterial blood flow can be well identified at each vasodynamic state. Furthermore, the changes of the flow velocities after vasoconstriction and -dilation were presented and interpreted in the entire physiological context. With this, the combined measurement of time-resolved blood flow and vessel diameter provides the basis to analyze the vascular function and its influence on the blood flow of small arteries of different mouse strains in response to different life styles.