Although the brain comprises only 2% of body weight, it receives 15% of cardiac output and consumes 20% of total body oxygen delivered through its blood vasculature. The brain blood vasculature consists of a highly branched vessel network that is tailored to efficiently deliver oxygen and nutrients to each brain region. However, little is known about how the brain vasculature develops. Using in vivo long-term serial confocal imaging of zebrafish larvae, we analyze this process and find that the developing midbrain vasculature undergoes not only vessel growth but also blood flow-driven vessel pruning. We show that vessel pruning occurs preferentially at loop-shaped vessel segments via the migration of endothelial cells to adjacent unpruned segments; over time, such vessel pruning reduces the complexity of the early primitive midbrain vasculature. We also observe that pruned vessel segments exhibit a lower and more variable blood flow than do unpruned segments and that the local blocking of blood flow triggers vessel pruning. By contrast, increases in blood flow impair vessel pruning. Finally, we show that pruning events can be predicted using a haemodynamics based mathematical model of the midbrain vasculature. These findings demonstrate the existence of brain vessel pruning during development and provide novel insights into the role of haemodynamics in brain vascular refinement.