The diagnosis of indolent systemic mastocytosis can be quite a challenge due to its wide spectrum of clinical manifestations. We are reporting a case of misdiagnosed indolent systemic mastocytosis in a 41-year-old male that has been wrongly treated first as a Non-Hodgkin lymphoma. The patient had generalized lymphadenopathy and eosinophilia, which are rare manifestations of indolent systemic mastocytosis. The chronic neglected pruritus and elevated tryptase levels along with histological findings were the main clues that have led us to the final diagnosis of indolent systemic mastocytosis. Later during the coronavirus disease 2019 pandemic, the patient presented with symptoms that are common between coronavirus disease 2019 and mast cell activation syndrome. Coronavirus disease 2019 was confirmed with a polymerase chain reaction test. There were no clear guidelines for managing a case like ours, so our management plan was based on the latest recommendations published at that time.