The industrial adoption of guided wave based Structural Health Monitoring (GWSHM) systems in aeronautics applications require the capability to understand the response of the system under uncertainties. These uncertainties are associated with environmental and operational conditions (EOC) such as changes in the ambient temperature, and the natural variability of a physical system. In this contribution effect of uncertainty on the damage size estimation is studied. Specifically, this work builds upon two previous contributions. First, experimental measurements from (Giannakeas, Sharif Khodaei, and Aliabadi 2022; Yue, Khodaei, and Aliabadi 2021) are used to extract the uncertainty of the health indicators (HI) and the localization algorithms. Then, the multi-fidelity damage estimation framework presented in (Giannakeas et al. 2023) is utilized that correlates the HI and damage location with a delamination damage size. A Monte Carlo sampling method is then used to propagate the uncertainty if the inputs to the damage size estimation and assess the response of the system for various levels of uncertainty. The uncertainties in both inputs can have a detrimental effect on the damage size estimation. The results indicate that a temperature difference of ΔT>10∘C during the computation of the HI can increase significantly both the mean and the standard deviation of the estimated area. Uncertainties in the location of damage on the other hand, does not seem to affect significantly the mean estimation however it does increase the standard deviation of the predictions.