In this study, an inverse algorithm based on the conjugate gradient method and the discrepancy principle is applied to estimate the unknown time-dependent base heat flux of a functionally graded fin from the knowledge of temperature measurements taken within the fin. Subsequently, the distributions of temperature in the fin can be determined as well. It is assumed that no prior information is available on the functional form of the unknown base heat flux; hence the procedure is classified as the function estimation in inverse calculation. The temperature data obtained from the direct problem are used to simulate the temperature measurements. The influence of measurement errors and measurement location upon the precision of the estimated results is also investigated. Results show that an excellent estimation on the time-dependent base heat flux and temperature distributions can be obtained for the test case considered in this study. (C) 2011 Elsevier Ltd. All rights reserved.