The Unit Hydrograph (UH) theory can be used to estimate the discharge hydrograph of a basin based on precipitation and runoff measurements. However, uncertainty in those measurements may unable a unique UH to be derived. It is well known that in comparison with runoff measurements, the spatial and temporal variability of rainfall is the main source of uncertainty. Hence, in this work we present a method to derive an improved unique UH assuming that the rainfall data is the main source of uncertainty. The Perturbed Rainfall Uncertainty Unit Hydrograph (PeRUUH) method is verified using a large scale rainfall simulator (LSRS). The method combines linear programming and reverse modelling to generate a perturbed rainfall intensity pattern, which accounts for the temporal and spatial rainfall uncertainty assuming discharge to be true. The method is validated in three different rainfall events using the LSRS. The PeRUUH method is more robust than the original UH, as it is shown to be able to estimate a unique UH for which the discharges have an error of (approx.) 10 times smaller than its counterpart.