Identifying emergent flux excitations and signatures of their mutual statistics with itinerant Majorana fermions remains a central challenge in Kitaev spin liquids. We show that an isolated π flux imprints an intrinsic Aharonov-Bohm-like interference pattern on the charge-neutral Majorana continuum. Spatially resolved scanning tunneling microscopy with inelastic electron tunneling spectroscopy (STM-IETS) probes this oscillation in the local dynamical spin response as a function of both bias voltage and tip-flux separation, reflecting the π phase acquired by Majorana trajectories encircling the flux. We show that large-scale exact diagonalization of the Kitaev honeycomb model and a complementary low-energy continuum theory yield consistent radial oscillations. These results provide a finite-energy, spatially resolved tunneling signature of a preexisting flux and a diagnostic of fermion-flux mutual statistics without requiring manipulation of individual anyons in the Kitaev spin liquid.