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An improved throughflow method to treat transonic viscous flows with shocks, using a finite-volume time-marching solver, is presented. Effects due to deviation, secondary losses, endwall skin friction and spanwise mixing are modelled. An alternative blade blockage is used to better take into account the effect of the blade on the transonic passage flow. A theoretical and numerical study of the axisymmetric shock showed that it is treated as a normal blade passage shock by the blade row model. Two different techniques to solve the numerical problems associated with the leading edge singularity due to incidence are investigated. The computation of an entire speed-line for a three stage transonic fan has been conducted in order to further calihrate and validate the various models. The validation showed that the solver is capable of giving a reasonable meridional picture of the transonic flow field for different operating points.