This paper presents a method for calculating the heat flux at the surface of a body from experimentally measured transient temperature data, which has been called the inverse heat conduction problem (IHCP). The analysis allows for two-dimensional heat flow in an arbitrarily shaped body and orthotropic temperature dependent thermal properties. A combined function specification and regularization method is used to solve the IHCP with a sequential-in-time concept used to improve the computational efficiency. To enhance the accuracy, the future information used in the sequential-in-time method and the regularization parameter are variable during the analysis. An example using numerically simulated data is presented to demonstrate the application of the method. Finally, a case using actual experimental data is presented. For this case, the boundary condition was experimentally measured and hence, it was known. A good comparison is demonstrated between the known and estimated boundary conditions for the analysis of the numerical, as well as the experimental data.