Born in Thessaloniki, Kitsiou started out playing for local teams and he joined Pavlos Melas at the age of 14. Having had trials with PAOK and Aris, he chose to join PAOK U20s, being discreetly influenced by his family. In PAOK U20s he got to feature in all positions except for goalkeeper and central defender. His adjustment skills were remarkable but he seemed more at ease at midfield.
Club career
PAOK
Kitsiou signed his first professional contract with PAOK in 2012 and took part in the seniors’ preseason in the summer 2012. Not 20 yet, he believed that he could help the team further. Kitsiou made his debut with PAOK in the Greek championship, participating in the win against AEK on 20 October 2012. He got to play in some matches, but not as many as he expected. However he made it to the deciding play-offs and was introduced in the right side of the defense, in the crucial last encounter against PAS Giannina. His performance along with his personality became his calling card as Huub Stevens was checking out his upgraded roster for 2013–14 season. In the preseason, he snatched the opportunity and Stevens rewarded him. He became the starting right full back for the 2013–14 season. In the 2013–14 season, Kitsiou scored his first goal with the club in a 4–1 home victory against Panionios. On 22 November 2013, PAOK announced its agreement with Stelios Kitsiou to extend his contract until 2018. Four days later he netted his first European goal against Shakhter Karagandy when substitute Salpingidis played a square pass for him to rifle high into the net from an angle. In the 2014–15 season Kitsiou playing in a mediocre, for him and the club, period 30 games in all competitions. He started the 2015–16 season as a starter. On 12 October 2015, he had a calf injury and will be out of action for three weeks, according to the club’s medical team. He started the 2016–17 season not as a first choice for the starting XI. On 11 January 2017 he scored in a 2–0 away Greek Cup win against Panetolikos He also scored in the Superleague Greece after almost three years in a 2–0 home win game against AEL.
On 26 June 2017, the details of Kitsiou borrowing to Belgian club Sint-Truiden are of interest as they prove that the deal is identical to what was done for Charis Charisis. The borrowing comes with a €1.2 million purchase option and 20% resale. Moreover, because Kitsiou contract is concluded in the summer of 2018, before the signing of the loan documents his contract with PAOK will be extended till the summer of 2019.
Ankaragücü
On 31 January 2019, Ankaragücü officially announced the signing of the Greek defender on a five-month loan deal. On 24 July 2019, Kitsiou made his move to Ankaragucu permanent after spending the second half of the season on loan in Turkey from PAOK. PAOK released an official statement announcing Kitsiou’s move. Kitsiou, who was on the books for PAOK for 12 seasons, signed a three-year contract with the Turksih club for an undisclosed fee. PAOK will receive a reported €200,000 for Kitsiou’s transfer. On 14 December 2019, in an 2–2 away draw game against giants Galatasaray he scored a late goal sealing a vital draw in his club effort to avoid relegation. It was his first goal with the club in all competitions.