CAAT director-general Chula Sukmanop said on Friday (March 20) that the rule applied to people of all nationalities, and airlines staff could decline to issue boarding passes to those who failed to do so.
The medical certificate must have been issued not more than 72 hours before departure.
Proof of insurance policies covering Covid-19 infection in Thailand, with coverage of at least US$100,000 per person, are also required from non-Thai passengers.
The new measures will be effective from 12.01am on March 21.
Thai passengers will have to show a medical certificate that they are fit to fly and also a letter issued by authorised state agencies certifying that they are Thai nationals returning to Thailand.