Clozapine is one of the most effective antipsychotic drugs, but its use is limited due to the possibility of severe side effects, such as neutropenia and agranulocytosis. The risk of these complications is the highest at the beginning of the treatment, but they can occur later, particularly when additional risk factors are present. In the described case, either COVID-19 vaccination or the infection itself led to severe neutropenia, which recurred during subsequent independent trials of other antipsychotic drugs. The paper presents the case of a 23-year-old woman diagnosed with early-onset, treatment-resistant schizophrenia who had been undergoing clozapine treatment with satisfying outcome for over 10 years. A week after the first dose of an mRNA vaccine against COVID-19, the patient developed a severe SARS-CoV-2 infection and experienced an extreme neutropenia, followed by a change of treatment. Although the patient fully recovered from the infection, the re-stabilization of her mental state remained unsatisfactory. The introduction of various newly implemented antipsychotic drugs led to partial improvement or another decline in the neutrophil count, despite discontinuing the use of clozapine. The authors discuss a few possible pathomechanisms. Based on our current knowledge, this is the first reported case of persistent neutropenia triggered by various antipsychotic drugs following exposure to SARS-CoV-2 antigens.