Solves the inverse problem of estimating the wall heat flux in a parallel plate channel, by using the conjugate gradient method with adjoint equation. The unknown heat flux is supposed to vary in time and along the channel flow direction. Examines the accuracy of the present function estimation approach, by using transient simulated measurements of several sensors located inside the channel. The inverse problem is solved for different functional forms of the unknown wall heat flux, including those containing sharp corners and discontinuities, which are the most difficult to be recovered by an inverse analysis. Addresses the effects on the inverse problem solution of the number of sensors, as well as their locations.