The effect of stochastic inflow fluctuations on the jet-switching characteristics of a harmonically plunging elliptic foil at a low Reynolds number regime has been analyzed in the present study. The inflow fluctuations are generated by simulating an Ornstein–Uhlenbeck process—a stationary Gauss–Markov process—with a chosen correlation function. In the absence of fluctuations, quasi-periodic movement of the wake vortices plays a key role in bringing out jet-switching at κh ≥ 1.5. However, fluctuating inflow alters the organized arrangement of the vortex street even at a lower κh (κh = 1.0), giving way to an advanced jet-switching onset. More frequent switching with a larger deflection angle is also observed at κh = 1.5 as compared to the no fluctuation case. Effects of inflow timescales on the deflection angle and switching frequency of the wake are investigated by varying the input correlation-lengths. The underlying flow physics are investigated through a qualitative study of the near-field interactions as well as various quantitative measures derived from the unsteady flow-field.