The San Andreas Fault System, one of the best-studied transform plate boundaries on Earth, is well known for its complex network of locked faults that slowly deform the crust in response to large-scale plate motions 1-8 . Horizontal interseismic motions of the fault system are largely predictable, but vertical motions arising from tectonic sources remain enigmatic. Here we show that when carefully treated for spatial consistency, global positioning system-derived vertical velocities expose a small-amplitude (±2 mm yr −1 ), but spatially considerable (200 km), coherent pattern of uplift and subsidence straddling the fault system in southern California. We employ the statistical method of model selection to isolate this vertical velocity field from non-tectonic signals that induce velocity variations in both magnitude and direction across small distances (less than tens of kilometres; ref. 9), and find remarkable agreement with the sense of vertical motions predicted by physical earthquake cycle models spanning the past few centuries 6,10 . We suggest that these motions reveal the subtle, but identifiable, tectonic fingerprint of far-field flexure due to more than 300 years of fault locking and creeping depth variability. Understanding this critical component of interseismic deformation at a complex strike-slip plate boundary will better constrain regional mechanics and crustal rheology, improving the quantification of seismic hazards in southern California and beyond.