German media reported earlier this month that two Germans had gone missing after arriving separately in Egypt in December.
Germany's foreign ministry on Friday confirmed the return of one German national and said another was still in Egyptian custody.
The families of both men believe their arrests were cases of mistaken identity. And Egyptian authorities had previously denied the arrests to AFP.
One man was detained at Cairo International Airport over suspicions he was seeking to join the IS jihadist group in Egypt's turbulent northern Sinai region, the Egyptian sources said. The suspect, who Germany said was 23, was reportedly arrested on December 27.
"Since he did not commit any crime under the Egyptian law and gave up the Egyptian nationality, the authorities decided to deport him to his country of nationality - Germany - in coordination with the German embassy," one of sources said.
A German foreign ministry spokesman confirmed that the man had arrived back in the country late Thursday.
The spokesman said the German embassy in Cairo had received confirmation that a second German, aged 18, was also being held and that the mission was seeking consular access to him.