Golay Complementary Sequence (GCS) is conventionally regarded as not applicable to blood flow detection due to potential side-lobe motion artifact in the decoding. In our previous study, it has been shown that GCS decoding can be performed by low-pass filtering in slow-time Doppler domain with cutoff frequency of PRF/4 to alleviate the motion artifact. In this work, the proposed GCS Doppler decoding has been implemented in a pre-clinical high-frequency ultrasound imaging system to study the color Doppler quality and signal-to-noise ratio (SNR) using phantom and in-vivo experiments. The phantom results show that, when the Doppler shift is within ±PRF/4, the GCS provides comparable Doppler information to conventional un-coded method while the SNR improves. The in-vivo results also demonstrate that Doppler penetration increases from 13.5 mm to 14.2 mm in the mouse's kidney. For the abdominal aorta, GCS Doppler also enables the increase of transmit frequency from 30 MHz to 35 MHz to detect blood flow.