Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) has caused a global pandemic resulting in many deaths. As a result, vaccines to prevent the onset of coronavirus disease 2019 (COVID-19) have been developed and have demonstrated high efficacy in large-scale clinical trials. Adverse events that develop within a few days after vaccination are common, such as fever, malaise, body aches, and headaches, and have become widely known as transient reactions. However, as COVID-19 vaccines are administered worldwide, several studies have highlighted that long-term side effects associated with vaccines against SARS-CoV-2 may include serious adverse events. There has been an increase in reports of COVID-19 vaccinations being associated with the onset of autoimmune diseases, such as anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis. This is a report of ANCA-associated vasculitis with periaortitis following the second dose of COVID-19 mRNA vaccination, in which a 56-year-old man developed numbness and pain in his lower extremities three weeks after COVID-19 vaccination. Following the onset of sudden abdominal pain, a fluorodeoxyglucose-positron emission tomography scan revealed periaortic inflammation. Serum myeloperoxidase (MPO)-ANCA levels were significantly elevated, and renal biopsy revealed pauci-immune crescentic glomerulonephritis. Treatment with steroids and cyclophosphamide alleviated abdominal pain and numbness in the lower limbs, resulting in a decrease in MPO-ANCA titers. The side effects of COVID-19 vaccination are still unclear. This report has indicated that side effects associated with vaccines against COVID-19 may include ANCA-associated vasculitis. However, a causal relationship between COVID-19 vaccination and the development of ANCA-associated vasculitis has not yet been clearly demonstrated. COVID-19 vaccination will continue internationally, so it is necessary to accumulate similar case reports in the future.