The COVID-19 pandemic resulted in a decline in outpatient attendance. Therefore, this study aimed to clarify long- and short-term clinic attendance trends by speciality in Japan between 2009 and 2021. A retrospective observational study of Japan’s claims between 2009 and 2021 was conducted using the Estimated Medical Expenses Database. The number of monthly outpatient claims in clinics was used as a proxy indicator for monthly outpatient attendance, and specialities were categorised into internal medicine, paediatrics, surgery, orthopaedics, dermatology, obstetrics and gynaecology, ophthalmology, otolaryngology, and dentistry. The annually summarised age-standardised proportions and the percentage of change were calculated. Joinpoint regression analysis was used to evaluate long-term secular trends. The data set included 4,975,464,894 outpatient claims. A long-term statistically significant decrease was observed in outpatient attendance in internal medicine, paediatrics, surgery, ophthalmology, and otolaryngology during the pandemic. From March 2020 to December 2021, which includes the COVID-19 pandemic period, outpatient attendance in paediatrics, surgery, and otolaryngology decreased in all months compared with that of the corresponding months in 2019. For some specialities, the impact of the pandemic was substantial, even in the context of long-term trends. Speciality-specific preparedness is required to ensure essential outpatient services in future public health emergencies.