Mavraj was promoted to the senior SV Darmstadt 98 side during the 2005–06 season, making his professional debut on 18 March 2006 against SC Pfullendorf in the Regionalliga Süd.

His strong performances in the first half of the season did not go unnoticed as he was called up by Germany U21 coach Dieter Eilts for a friendly against Italy in February 2007.

On 29 January 2011 he made his debut at the 2–2 draw against Alemannia Aachen at New Tivoli stadium, coming on as a substitute for Stephan Schröck in the 90th minute.

[5] He was elected captain by his teammates in a secret ballot, finishing ahead of Thomas Kleine, Gerald Asamoah, Stephan Fürstner and Milorad Peković.

[citation needed] On 3 March 2014, Mavraj scored the victory goal for his team against FSV Frankfurt and Greuther Fürth managed to win three gold points that keep the race for the return to the Bundesliga.

Mavraj had declared early that if Greuther Fürth didn't win promotion to the Bundesliga for the next season, he would leave the club after his contract expired on 30 June 2014[10] and on 19 May 2014, 2.

[11] On 19 December 2015, Mavraj returned to the football fields after seven months absence, playing the last minutes in the 2–1 triumph over Borussia Dortmund in Bundesliga.

On 27 December 2016, Mavraj signed with fellow Bundesliga team Hamburger SV until 30 June 2019 for a transfer fee of reportedly €1.8 million.

He started applying for the Albanian citizenship in September 2006 along with Besart Berisha, Genc Mehmeti and Alban Dragusha, following the recommendations of Hans-Peter Briegel before he resigned from his role as the manager of the Albania national team.

FSHF gave Mavraj a chance to play international football at a senior level by permitting the Albanian manager at the time Josip Kuže to call him up for a friendly in Tirana against Northern Ireland on 3 March 2010.

However, just one day prior to the team meeting up to begin preparing for the game Mavraj backed down and did not show up, much to the dislike of the FSHF and the Albanian fans, who accused him of being a traitor for rejecting Albania twice.

[30] The sudden change of mind regarding his international call up was reportedly due to a conversation he had on the phone with Matthias Sammer, who was technical director of the German Football Association at the time.

Sammer told Mavraj that he may have a future with the Germany national team and that he would be considered for an invitation to the senior side after the 2010 FIFA World Cup.

He made it his first official debut for Albania on 7 September 2012 in the opening match of the 2014 FIFA World Cup qualification Group E against Cyprus, playing the full 90 minutes, which finished in the home 3–1 victory.

[33] Mavraj missed out 7th and 8th matches in September 2013 due to the injury but recovered in time for two last games against Switzerland and Cyprus on 11 and 15 October 2013.

[36] Mavraj started another qualification campaign, the UEFA Euro 2016 qualifiers, as on 7 September 2014 he played a full 90-minutes match in the 1–0 away victory against Portugal.