Ibraimi was born in Tetovo, SR Macedonia, to Albanian parents. While growing up in Tetovo, Agim joined the Shkendijayouth team and eventually broke through into the senior squad at the age of 17.
Ibraimi debuted for Shkendija in 2005 and was a crucial member of the team. He made forty nine appearances and scored three goals, helping Shkendija reach fifth place in the Prva Liga. Making a significant impact on the club at such a young age, Agim was picked up by Red Bull Salzburg and moved abroad. At Red Bull Salzburg, Ibraimi developed further under their tutelage. In two years at Salzburg, Ibraimi made three appearances for the senior team.
Ibraimi joined Olimpija who were at that time playing in the Slovenian Second League. His first season in the Slovenian capital was very successful, as Olimpija finished as league winners with Ibraimi scoring eleven goals. The start of his second season in Ljubljana was not as smooth. After Miran Pavlin, the director of football who brought him to the club, departed for Koper, Ibraimi wanted to join him. But Olimpija's board had none of it, as the player still had a valid contract with the club. The start of his first season in Slovenian PrvaLiga was difficult, his form was not up to standard, but it did pick up eventually and Ibraimi regained his place in Olimpija's first eleven. He scored his first goal in the Slovenian PrvaLiga on 28 August against Koper.
Eskisehirspor
Ibraimi terminated his contract with Olimpija in the summer of 2010 and signed a three-year deal with Turkish team Eskişehirspor on 3 September 2010. He made his debut for Eskisehirspor on 25 September 2010 when he came off the bench in the 77th minute, but his team lost 1–0. Ibraimi failed to adjust to the Turkish league so he and the club agreed to mutually terminate the contract and Ibraimi joined Nafta Lendava during the 2011 January transfer window.
On 10 June 2011, it was announced that Ibraimi has signed a three-year contract with the Slovenian club Maribor. He made his debut for Maribor against Dudelange in the qualifying rounds of the Champions League where he also scored his first goal and assist for the club. Ibraimi has been a regular starter for Maribor and has been having a tremendous season in the Slovenian PrvaLiga. Despite not qualifying past the third round of qualifications, Maribor had a chance in the play offs for the UEFA Europa League against Scottish club, Rangers. Ibraimi helped Maribor reach the group stages of the Europa League after scoring a goal from just inside the box in the first leg. Despite Maribor getting last place in their group, Ibraimi scored against Portugal club, SC Braga, in the only match of the group stage where Maribor secured a point. In May 2012, Ibraimi signed a new contract with the club until May 2015. In the same month, he scored directly from a corner kick in an 8–0 win against Triglav Kranj and won the league title with Maribor. In December 2012, he won the Macedonian footballer of the year award. He was voted as one of the best midfield players in the 2012–13 Slovenian PrvaLiga alongside his teammate Goran Cvijanović and Nik Omladič. He was also selected as the overall best player in the 2012–13 PrvaLiga season.
On the 31st of August, 2013, Agim Ibraimi moved to Cagliari on loan in exchange for Pablo Ceppelini and money. In his second game for Cagliari, he provided an assist against Inter Milan. On March 2, 2014, Ibraimi scored his first goal for Cagliari against Udinese and providing an assist eight minutes earlier. Only maintaining five starting appearances for Cagliari, he did not receive much playing time in Italy. Agim Ibraimi has reached an agreement with Maribor to extend his contract until May 2017.
Maribor
Returning to Maribor, Ibraimi helped the club reach the UEFA Champions League group stage by scoring in the qualifying rounds against Zrinjski Mostar and Maccabi Tel Aviv. The last time Maribor were in the Champions League was in 1999. On 5 November 2014, Maribor drew against Chelsea in the Champions League. Ibraimi scored on the 50th minute with a brilliant curling effort from the edge of the box.
Ibraimi is multilingual, speaking six languages fluently: Albanian, English, German, Macedonian, Serbo-Croatian and Slovenian. Ibraimi is a cousin of professional football player Arijan Ademi. In February 2016, after having spent years of playing in the country, Ibraimi received a Slovenian citizenship.