Developing accurate and efficient solutions for inverse heat conduction problems allows advancements in the heat flux measurement techniques for many applications. In the present paper, a one-dimensional medium with a moving boundary is considered. It is assumed that two thermocouples are used to measure temperature at two locations within the medium while the front boundary is moving towards the back surface. Determining surface heat flux using measured temperature data is an inverse heat conduction problem. A filter based Tikhonov regularization method is used to develop a solution for this problem. Filter coefficients are calculated for various thicknesses of the medium. It is demonstrated that the filter coefficients can be interpolated to calculate the appropriate values for each thickness while it is continuously moving at a known rate. The use of filter method allows near real-time heat flux estimation. The developed solution is validated through several numerical test cases including a test case for a moving boundary in a medium modeled in COMSOL. It is shown that the proposed solution can effectively estimate the surface heat flux on the moving boundary in a near real-time fashion.