Vector Dark Matter (VDM) that couples to lepton flavor (Le, Lµ, Lt) acts similarly to a chemical potential for the neutrino flavor eigenstates and modifies neutrino oscillations. VDM imparts unique signatures such as time and directional dependence with longer baselines giving better sensitivity. We use the non-observation of such a signal at Super-Kamiokande to rule out the existence of VDM in a region of parameter space several orders of magnitude beyond other constraints and show the projected reach of future experiments such as DUNE.