This work presents a double sliding mode control designed for accelerating the measurement of heat fluxes using thermopiles. The slow transient response generated in the thermopile, when it is placed in contact with the surface to be measured, is due to the changes in the temperature distributions that this operation triggers. It is shown that under some conditions the proposed controls keep the temperature distribution of the whole system constant and that changes in the heat flux at the thermopile are almost instantaneously compensated by the controls. One-dimensional simulations and experimental results using a commercial thermopile, showing the goodness of the proposed approach, are presented. A first rigorous analysis of the control using the Sliding Mode Control and Diffusive Representation theories is also made.