SARS-CoV-2 infection can lead to pathological disorders in various organs due to the ubiquitous of angiotensin-converting enzyme 2 (ACE2), which serves as a receptor for SARS-CoV-2. However, tissue damage may not only be the result of viral infection. SARS-CoV-2 has been shown to induce the production of autoantibodies to ACE2, and their presence is associated with disease severity. The spleen is one of the targets for COVID-19. The presence of ACE2 in the red pulp sinus endothelium cells of the spleen and in tissue-resident CD169+ macrophages positioned in the splenic marginal zone makes these cells a potential target of autoimmune reactions to ACE2 triggered by SARS-CoV-2. In addition, antibodies to the SARS-CoV-2 S protein cross-react with a wide range of human tissue proteins and can cause tissue damage. The most common splenic pathologies in deceased COVID-19 patients are lymphocyte depletion and subsequent hemaphagocytosis. Since the spleen plays a fundamental role in the immune response regulation, splenic damage could be one of the causes of immune perturbations associated with severe COVID-19. To test the hypothesis of the autoimmune nature of COVID-19, we developed a non-infectious experimental model of autoimmune multiorgan damage caused by immunization with SARS-CoV-2 S protein. The purpose of this work was to study the spleen in rats with induced multiorgan damage caused by immunization with SARS-CoV-2 S protein, as well as the influence of pre-existing autoimmune disease on the severity of splenic damage caused by an immune response against S protein. Intact Wistar rats and Wistar rats with completed experimental autoimmune encephalomyelitis were immunized with S protein in incomplete Freund’s adjuvant (IFA). Control rats received an injection of IFA. No changes were detected in the secondary follicles number in the spleen of rats immunized with the SARS-CoV-2 S protein. However, in the spleen of rats with previously induced autoimmune encephalomyelitis, immunization with SARS-CoV-2 S protein caused a significant decrease in the number of secondary follicles relative to the control group. Hemosiderin deposits and macrophage hyperplasia of the marginal zones of the white pulp were detected in both groups immunized with S protein. Thus, immunization with the S protein of SARS-CoV-2 causes changes in the spleen of rats similar to those detected in patients who died from COVID-19. Damage to the spleen is more varied and pronounced in rats with previous experimental encephalomyelitis.