On 16 February 2020, Vagiannidis made his professional debut and scored his first goal, getting an assist as Panathinaikos beat Panetolikos 3–1 at the Olympic Stadium.
In May 2020, Italian giants Inter expressed interest in acquiring the talented young player of Panathinaikos.
The 18-year-old right-back had recently reached a verbal agreement with Panathinaikos to sign a new contract before talks were halted due to the Coronavirus pandemic.
[4] On 3 February 2021, he made his debut with the new club in Belgian Cup against Lokeren-Temse at the Daknamstadion in the season 2020–21.
[5] On 3 September 2021, Panathinaikos officially announced the return of Georgios Vagiannidis, who signed on a free transfer, a four-year contract with the club for an undisclosed fee.