Author summary Transposable elements (TEs) are engines of evolution over short and long evolutionary time scales and have played crucial roles in pathogen evolution. The impacts of TEs are multifaceted, ranging from creating adaptive sequence variants, gene disruptions, chromosomal rearrangements or even triggers of genome expansions. As a defense, pathogen genomes have evolved sophisticated mechanisms to silence or mutate TEs. Pathogens have also benefited from TEs thanks to altered virulence genes and increased antifungal resistance. How TEs cope with genomic defenses and expand in genomes (i.e., cause TE bursts) remains poorly understood though. We analyzed over a dozen high-quality genomes of a fungal wheat pathogen species, which has recently experienced TE reactivations. We reconstructed the evolutionary history of many TEs by building phylogenetic trees. Using this approach, we identified "invasion routes", i.e., tracking TE copies that constitute the most likely ancestors of renewed activity of TEs (i.e. a bursts). Our work showed that specific features, in particular the proximity to genes, were likely important drivers leading the reactivation of TEs.