Fourier-domain optical coherence tomography (FD-OCT) is a non-invasive imaging technique which allows the in vivo examination of subsurface tissue. Besides the structural imaging, FD-OCT is capable to measure blood flow velocities. This method is referred to as phase-resolved Doppler FD-OCT and often used in small retinal vessels (diameters about 100 μm) with low blood flow velocities. In this study, we present a FD-OCT system with a spectrum read-out rate of 11.88 kHz showing the ability to assess velocity profiles in the in vivo mouse model with blood vessels up to a diameter of 300 μm. Before realization of the in vivo study on such large vessels, an in vitro flow phantom using a 1% Intralipid solution as well as whole human blood flowing through a 320 μm glass capillary was constructed. The velocity profiles of the Intralipid flow can be measured entirely. Due to the large diameters of the capillary and the investigated murine vessels, entire flow profiles cannot be measured when using whole blood. But the flow can be estimated by fitting a parabolic velocity profile to the onset of the measured data. With this method, it is possible to analyze the systolic and diastolic arterial as well as the venous blood flow. To our knowledge this was the first time that blood flow velocities of vessels with inner diameters of about 300 μm in the in vivo mouse model were assessed by phase-resolved Doppler FD-OCT.