Increased numbers of patients with secretory otitis media appeared in outpatient clinics after the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Omicron pandemic; however, the relationship between SARS-CoV-2 Omicron variant infection and secretory otitis media is uncertain. We performed tympanocentesis and used reverse transcription-polymerase chain reaction (RT-PCR) testing to examine middle ear effusion (MEE) and nasopharyngeal secretions from 30 patients with secretory otitis media associated with SARS-CoV-2 infection. RT-PCR was performed using the open reading frame 1ab and nucleocapsid protein gene kit from Shanghai Berger Medical Technology Co., Ltd., as the sole assay method, in accordance with the manufacturer's instructions. MEEs from 5 of the 30 patients tested positive for SARS-CoV-2, including one patient with positive results for both the nasopharyngeal secretion and MEE. We report and discuss the medical records of six patients, including these five MEE-positive patients and a MEE-negative patient. SARS-CoV-2 RNA can be detected in MEE caused by coronavirus disease 2019-related secretory otitis media even when a patient's nasopharyngeal secretion tests PCR-negative for SARS-CoV-2. The virus can remain in the MEE for a long time after SARS-CoV-2 infection.