The aim of this work was to investigate the effect of pre-infection with bovine viral diarrhoea virus (BVDV) on thymus immune cells from calves challenged with bovine herpesvirus 1 (BHV-1). Twelve Friesian calves, aged 8 to 9 months, were inoculated with non-cytopathic BVDV-1. Ten of them were subsequently challenged with BHV-1 and euthanized in batches of two at 1, 2, 4, 7 or 14 dpi with BHV-1. The other two calves were euthanized prior to the second inoculation and were used as BVDV-infected controls. A further 10 calves were inoculated solely with BHV-1 and euthanized at the same time points. Two calves were not inoculated with any agent and were used as negative controls. Quantitative changes in immune cells were evaluated with immunohistochemical methods to compare coinfected calves and calves challenged only with BHV-1. The results of this study pointed out BVDV as responsible for the thymic lesions observed in the experiment as well as for the majority of immunopathologic changes, including a downregulation of Foxp3 lymphocytes and TGFβ, which reverted as BVDV was cleared, and an overexpression of medullary CD8+ T cells. However, despite not inducing evident lesions in the thymus, BHV-1 seemed to prompt some immune alterations. Collectively, these data contribute to the knowledge on the immunopathologic alterations of the thymus during BVDV infections, and its importance in the development of secondary infections.