Vatnikaj joined his hometown club Partizani Tirana at the age of 10 in 2005 where he progressed through the club's youth teams before joining local rivals Tirana in 2011, where he initially played for the club's under-17 side. After one season with the under-17s, he was promoted to the under-19s at Tirana but he left the club in January 2013 and returned to Partizani Tirana, where he also played for the club's under-19s side.
On 11 September 2017, Vatnikaj officially joined Albanian First Division side Bylis Ballsh by penning a one-year contract. He was presented along with his brother Junild. He made his debut five days later in the opening match of 2017–18 Albanian First Division against Shkumbini Peqin, finished in a 2–0 away win. He scored his first goal of 2017–18 season on 25 November in the matchday 9 against Apolonia Fier as Bylis was defeated 3–1.
In the deadline day of winter transfer window, Vatnikaj become a player of fellow First Division side Kastrioti Krujë for an undisclosed fee. He played his first match for the club later on 10 March 2018 by entering in the final minutes of a goalless draw versus Besëlidhja Lezhë. He opened his scoring account on 21 April in the 1–1 draw at Dinamo Tirana. Kastrioti eventually finished top in the Group A, meaning that they have secured a top flight spot for the next season. In the final versus the Group B winner Tirana, Vatnikaj entered in the last 14 minutes as Kastrioti lost 2–0 at Elbasan Arena.
Later in 2011 he was promoted to under-17 side, being called-up by manager Džemal Mustedanagić for the qualifying games of 2012 UEFA European Under-17 Championship in October. He made his first appearance for the team in the opening qualifying match versus Slovakia, coming on as a late replacement for Frans Ymeralilaj, who had given Albania the win thanks to his brace. He went on to play another against Estonia which ended in a 1–1; this result secured Albania a place in the elite round of the European Championship for the first time in 9 seasons. In the elite round, Vatnikaj continued to be a substitute, appearing only in the last minutes as Albania was eliminated after finished 3rd in Group 5.
Under-19
– Vatnikaj was part of national team in two matches against Moldavia.
Under-21
In November 2014, Vatnikaj participated with Albania U21 in the friendly tournament held in Dubai. He scored in the first match against Bahrain that was won by Albania 3–2. Later in March 2015, Vatnikaj was called-up again for the opening 2017 UEFA U21 Championship qualifier against Liechtenstein on 28 March 2015. He was given the number 11 shirt and started the match partnering Rey Manaj in attack. He played only in the first half as the 2–0 away victory saw Albania off to a winning start.
Personal life
His brother Junild is also a professional footballer who plays at Bylis Ballsh.
