AbstractA time‐dependent heat conduction problem can be solved by the method of fundamental solutions using the fundamental solution to the modified Helmholtz equation or the fundamental solution to the heat equation. This paper presents solutions using both formulations in terms of initial and boundary conditions. Such formulations enable calculation of errors and variance, which indicates sensitivities of solutions to uncertainties in initial and boundary conditions. Both errors and variance of solutions to three test problems by the two methods of fundamental solutions are used to compare performances of the methods. Copyright © 2005 John Wiley & Sons, Ltd.