An airplane landed at the Vilnius International Airport on Monday afternoon, bringing back 90 Novaturas and 82 Tez Tour passengers.
Another 50 should stay in Egypt until Aug. 26.
About 800 people have been killed in Egypt in recent days during clashes between security forces and supporters of the ousted president, Mohammed Morsi.
Egypt's government has declared a nationwide state of emergency and a nighttime curfew in many provinces.
Lithuania's Foreign Ministry has advised against trips to the North African country.