Professionally he has played for Omonia, Kavala, Fokikos, Iraklis, PAS Giannina, AEK and lithuanian FK Sūduva.

The 25-year old goalkeeper Giannikoglou, who only made four Super League appearances with PAS Giannina in the 2017–18 campaign, has signed a three-year deal with AEK after his PAS Giannina's contract reached its conclusion.

“I am delighted to work with Vasilis Barkas and Panagiotis Tsintotas, the goalkeepers which made AEK champions alongside Giannis Anestis.

It’s a great incentive for any Greek footballer to wear the AEK shirt, my goal is to work hard and be ready for when I receive a chance.”[5] On 13 June 2019, Giannikoglou returned to PAS Giannina.

Giannikoglou debuted for Greece U17 in 2009 in a friendly match against Belarus national under-17 football team.