Using a systems immunology approach, this study comprehensively explored the immunopathogenesis of Peste des Petits Ruminants (PPR) focussing on strain-dependent differences in virulence. Saanen goats were infected either with the highly virulent Morroco 2008 (MA08) or the low virulent Ivory Coast 1989 (IC89) strain of PPR virus (PPRV). As expected, MA08-infected goats exhibited higher clinical scores, pronounced lymphocyte depletion, and lesions affecting mucosal and lymphoid tissues. CD4 T cells were found to be most affected in terms of depletion and infection in the peripheral blood. Transcriptional analyses of the blood and lymphoid tissue demonstrated activation of interferon type I (IFN-I) responses at three days post infection (dpi) only with MA08, but comparable IFN-I expression levels with MA08 and IC89 at 6 dpi. In contrast, only the MA08 strain induced strong inflammatory and myeloid cell-related transcriptional responses which as observed in tonsils but not in the mesenteric lymph node. This inflammatory response in the tonsil was associated with an extensive damage and infection of the tonsillar epithelium in the crypts, pointing on a barrier defect as a possible cause of inflammation. The other prominent effect induced by MA08, but not IC89, was a strong and early downregulation of cell cycle gene networks in lymphoid tissues. This effect was found in the blood compartment and all analysed lymphoid tissues and can be interpreted as suppressed lymphocyte proliferation that may cause immunosuppression during the first week following MA08 infection. A proteome analysis confirmed elevated synthesis of IFN-I response proteins during infection with both strains, but only the MA08 strain additionally upregulated ribosomal and inflammation-related proteins. In conclusion, the present comprehensive investigation delineates strain-dependent differences in early immunopathological processes associated with severe inflammation disease and a blunted lymphocyte proliferation. Understanding such strain-specific differences is relevant for effective PPRV surveillance strategies.