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The Visit Portugal COVID page list the following rules which are currently in effect. Of course, these rules could change at any point as the situation progresses. (Bold emphasis is mine.)
Flights to and from Portugal Air travel to and from Portugal is allowed to:
- European Union countries;
- Schengen Associated Countries - Liechtenstein, Norway, Iceland, Switzerland β and the United Kingdom;
- Australia, Canada, China, South Korea, Georgia, Japan, Morocco, New Zealand, Rwanda, Thailand, Tunisia, Uruguay.
Flights to and from other destinations will only be permitted for essential travel. βEssential travelβ is defined as trips allowing the transit, entry into and departure from Portugal for the following persons:
- citizens of a European Union member state, Schengen Associated countries and their family members;
- citizens repatriated through consular assistance;
- third-country nationals travelling for professional purposes, study, family reunions, health and humanitarian reasons and under the reciprocity principle.
On essential journeys, passengers must present a negative test to COVID-19 (RT-PCR), carried out within 72 hours before departure time. This test is not asked in Portugal for those who are in transit and do not have to leave the airport facilities.
In short, as someone who is transiting through Portugal from a non-allowed/other destination for the essential purpose of studying, you are permitted to transit through Portugal. Portugal does not require any COVID-19 testing if you do not leave the airport.