Real problems in science and engineering generally do not have an analytical solution, which invariably leads to the application of numerical methods to analyze the problem. The numerical solutions to the same problem give different results due to variations in discretization, which are defined as simulation noise in this study. Microfluidics impedance flow cytometry is employed to demonstrate and compare experimental and simulated noise. For measurement of the simulation noise, an object is assigned with the same electrical parameters as the medium and moved along the electrode region through a microchannel. Since the object is no different to the medium in terms of material properties, forwarding of the object through the electrodes doesn't have any physical effect, but just reorders the meshing. However, the impedance, which is the calculated output parameter of the simulation, fluctuates due to the reordering of the meshes and is defined as the simulation noise. By employing the imaginary object method, noise can be measured for every Finite element method (FEM) simulation even if the problem has a different physical background.