Skondras began his career in 2004 with Asklipios Trikalon and joined after only one year in July 2005 with Atromitos. In July 2008 was promoted to the senior team who played in the Beta Ethniki here earned his first professional match on 30 November 2009 against Diagoras. Skondras gave a solid performance for Atromitos in 2011/12 Greek Cup where he virtually kept then top-scorer Kevin Mirallas quiet for most of the evening; a display that prompted plenty of interest from the Olympiakos brass. The Greece U-21 international was rumored to be on his way to the Giorgos Karaiskakis Stadium this past summer as doubt over Vasilis Torosidis’ future at the club circled the port city. When speculation regarding Torosidis' departure for Roma died down, the pursuit of Skondras was abandoned for a while.
On 21 June 2013, Skondras, left Atromitos to sign a four-year contract with PAOK for the sum of €300.000. He made his debut with the club on 17 August 2013 in a 3–0 home win against Xanthi. On 16 April 2014 in a semi-final for the Greek Cup against Olympiakos where the game is held up for over an hour after fans throw hundreds of flares onto the pitch and set fire to a dug outs has a key role in a 1–0 win following a 2–1 defeat in the first leg in Athens helping PAOK eventually went through the final. Giannis Skondras experienced two defeats in Greek Cup finals during his spell at Atromitos. His third attempt to silverware –with the black-and-white kit this time round- is nearing and he believes that he will be lucky that time. Unfortunately, Skondras did not manage to win the Greek Cup in his third presence on it as his club lost 1–4 against Panathinaikos. In a mediocre 2014–15 season with the club, he had his best professional year so far with 37 appearances in all competitions. On 8 October 2015, rumour transfers for a possible move of the player in the rivals Panathinaikos, are rejected by the club as the Greens do not intend to make a move for the 25-year-old right back since they want to support the players that are already chosen for the teams' roster. The 2016–17 season did not start well for the 26-year-old international as the Serbian manager Vladimir Ivić did not include him in his team's pre-season squad and it seems that Giannis Skondras will be finally released from the Greek club this summer, after three seasons and 93 official performances with two goals. On 26 January 2017, PAOK officially announced the mutual termination of the Greek right defender contract, six-month before its actual expiration.
Skondras signed a short-term contract with Scottish Premiership club Hamilton Academical in January 2017. On 8 April 2017, in his 8th appearance for the club, he was dismissed just before half time for a foul on the counter-attacking Ryan Dow at home to Ross County. The decision was later overturned following an appeal. On 20 May 2017, Skondras scored his first goal for the club with a thunderous long-range strike in a 4–0 win against Dundee, a result that meant Hamilton avoided automatic relegation to the Scottish Championship. Accies announced in June 2017 that Skondras had decided to leave, but he changed his mind and signed a new one-year contract in July. On 16 December 2017, in a 3–2 home win against Ross County, following a foul by Hamilton's Georgios Sarris on Davis Keillor-Dunn which led to a touchline confrontation between players from both sides, Skondras was sent-off having raised a hand towards Ross County defender Kenny van der Weg. During the incident he also appeared to man-handle an assistant referee. Two days later he was charged with excessive misconduct by the Scottish Football Association. On 30 March 2018, Skondras was released by Hamilton.
Lamia
On 4 September 2018, Skondras returned to the Superleague, joining Lamia on a free transfer. On 11 November 2019, he scored a brace in a crucial 3–0 away win against AEL.
