There is a growing body of evidences for the presence of crystalline material in comets. These crystals are believed to have been annealed in the inner part of the proto-solar Nebula, while comets should have been formed in the outer regions. Several transport processes have been proposed to reconcile these two facts; among them a migration driven by photophoresis. The primarily goal of this work is to assess whether disk irradiation by a Pre-Main Sequence star would influence the photophoretic transport. To do so, we have implemented an evolving 1+1D model of an accretion disk, including advanced numerical techniques, undergoing a time-dependent irradiation, consistent with the evolution of the proto-Sun along the Pre-Main Sequence. The photophoresis is described using a formalism introduced in several previous works. Adopting the opacity prescription used in these former studies, we find that the disk irradiation enhances the photophoretic transport: the assumption of a disk central hole of several astronomical units in radius is no longer strictly required, whereas the need for an ad hoc introduction of photoevaporation is reduced. However, we show that a residual trail of small particles could annihilate the photophoretic driven transport via their effect on the opacity. We have also confirmed that the thermal conductivity of transported aggregates is a crucial parameter which could limit or even suppress the photophoretic migration and generate several segregation effects. (C) 2015 Elsevier Inc. All rights reserved