Protest leader Akis Poullos told the Associated Press that demonstrators are demanding the closure of RAF Akrotiri, from where four British Tornado warplanes took off to take part in Friday night's missile strike.
Poullos said Sunday's demonstration also wanted to send the message to the Greek Cypriot administration not to lend any assistance to "imperialist attacks" on Syria and to demand an end to the war in the country.
Protesters used red paint to write "NATO killers go home" on a nearby wall outside the base's gate.
Former colonial overseer Britain retained RAF Akrotiri and another military base on Greek Cyprus after the east Mediterranean island gained independence in 1960.
The Greek Cypriot administration said that it wasn't given any forewarning about Saturday's airstrikes.
It also said British Prime Minister Theresa May assured Greek Cypriot leader Nicos Anastasiades that there's no danger to the island and that Cypriots can feel secure.