The current study aimed to describe the use of antipsychotics to clarify the gap between clinical guidelines and health care practice in Japan. We used data from the JMDC Claims Database (JMDC Inc., Tokyo, Japan), a nationwide claims database, from 2005 to 2016. Antipsychotics were defined as drugs coded as N05A with the Anatomical Therapeutic and Chemical (ATC) codes. We described the annual changes in proportions based on the number of patients prescribed any antipsychotics. From the database of 4,081,102 people, the data of 12,382 patients was extracted by applying the following exclusion criteria: no use of antipsychotics, missing the prescription date or dose, inpatients, prescribed antipsychotics only for use as needed, prescribed only injectable antipsychotics except for long-acting injections (LAIs), without schizophrenia as the primary disease, not exceeding 75 mg/day chlorpromazine equivalent, and less than 18 years old. The use of second-generation antipsychotics (SGA) has been expanding, while the use of first-generation antipsychotics has been decreasing. Aripiprazole accounted for the highest proportion of prescribed antipsychotics (31.9%) in 2016. Even though clozapine is categorized as a SGA, it accounted for a paltry 0.2%. The proportion of prescribed antipsychotics accounted for by LAIs was less than 5%. Although the use of antipsychotics for schizophrenia in Japan mostly corresponds to various clinical guidelines, limited use of clozapine and LAIs was identified. Further research focusing on the factors affecting the prescription of these underused antipsychotics may help advance the pharmacological therapy of schizophrenia.