This paper presents an application of the Global Sensitivity Analysis (GSA) method in evaluating performance of impedance measurement algorithms implemented in modern Intelligent Electronic Devices (IEDs) when affected by uncertainty. To be specific, the GSA is applied in testing an algorithm for distance protection of a single transmission line in a system with two lines on the same towers. Factors contributing to uncertainty are discussed in the paper. The GSA method decomposes variance of the estimation error according to the factors and their interactions, and in this way identifies the factors that have the highest impact on the estimation error. Computation of the GSA sensitivity indices relies on the Quasi-Monte Carlo (QMC) technique with Sobols quasi-random sampling. This is timeconsuming for large number of factors therefore, fast pre-screening process based on the Morris method is implemented to remove non-influential parameters and reduce the factor space before running the QMC. The methodology is implemented using fault simulation software DIgSILENT PowerFactory to calculate fault impedance as a function of uncertain parameters (i.e. factors) as well as voltage and current signals that are inputs to an IED under test. In this simulation, factor space is sampled using Sobols quasi-random sequence generated with the standard GSA software tool called SIMLAB. All simulations of the transmission line faults for various parameter values and calculation of the performance indices (i.e. sensitivities) is automated using the program developed in DIgSILENT Programming Language (DPL). This testing technique is applied to study the fault impedance measurement implemented in SEL-421.