Multiphase flows through reservoir rocks are a universal and complex phenomenon. Relative permeability is one of the primary determinants in reservoir performance calculations. Accurate estimation of the relative permeability is crucial for reservoir management and future production. In this paper, we propose inferring relative permeability curves from sparse saturation data with an ensemble Kalman method. We represent these curves through a series of positive increments of relative permeability at specified saturation values, which guarantees monotonicity within, and boundedness between 0 and 1. The proposed method is validated by the inference performances in two synthetic benchmarks designed by SPE and a field-scale model developed by Equinor that includes certain real field features. The results indicate that the relative permeability curves can be accurately estimated within the saturation intervals having available observations and appropriately extrapolated to the remaining saturations by virtue of the embedded constraints. The predicted well responses are comparable to the ground truths, even though they are not included as the observation. The study demonstrates the feasibility of using ensemble Kalman method to infer relative permeability curves from saturation data, which can aid in the predictions of multiphase flow and reservoir production.