The first appearance of AEK Athens in European competitions was in the Balkans Cup of the 1960–61 season alongside Steagul Roșu Brașov, Levski Sofia, Partizani Tirana and Fenerbahçe.

After 4 matchdays, they achieved 1 win 1 draw and 2 defeats, and when Steagul Roșu Brașov secured the title, AEK withdrew from the tournament, with the remaining games being awarded to their opponents.

The first appearance in a UEFA match quickly turned into a nightmare, as they faced a 7–2 defeat at Stade Municipal du Ray, with a four-goal performance by Lucien Cossou and the goals of Yvon Douis and Karimou Djibrill with the Greek side reducing with Kostas Nestoridis and Fanis Tasinos.

In order for a free date for the match to be found, 7 months had to pass and at Mithat Paşa, AEK were defeated by 3–1 and a lost a great opportunity to win an international trophy.

At the first match at Spartak Stadium, Branko Stanković set the team to maintain a favourable score for the rematch and despite withstanding the pressure by the Czechoslovaks, they conceded two goals with Jarábek and Kabát, but they managed to reduce their lead with Sevastopoulos and achieve their target.

The team were left with only a few minutes to take the match to the extra time and despite their intensive pressure the ball eventually did not end up in the net and AEK were eliminated from the tournament achieving one of the greatest campaigns in their history.

In the first match at San Siro, AEK managed to take the lead with Pomonis, but Inter's superiority was obvious and turned the game to 4–1 with Jair, Mazzola, Facchetti and Boninsegna.

In Romania, AEK presented a mediocre appearance, which was largely due to the tragic condition of the field and lost by 1–0, but in the replay match with an imposing performance they were qualified with a 3–0 victory.

In the first leg at Nea Filadelfeia, the Greek side achieved their greatest ever victory in the tournament and tearing their opponents by 6–1 with a brace of Dušan Bajević and the goals of Christos Ardizoglou, Tasos Konstantinou, Lakis Nikolaou and Thomas Mavros, with the Portuguese reducing with António Oliveira.

In 1989, having won their first championship after 10 years, AEK returned in the European Cup playing against Dynamo Dresden where, despite the defeat in Germany by 1–0, with a magical performance in the rematch, were qualified with an incredible 5–3 victory with Manolas, Okoński, Savvidis and Savevski being the scorers for the Greek side.

In the next matchday Ajax came to Greece with all their stars and despite the pressure from the Dutch, AEK surprisingly took the lead with Savevski, however the team of Van Gaal quickly responded and eventually turned the game to the final 1–2 with Litmanen and Kluivert.

The now suspected Milan, welcomed AEK to the Stadio Nereo Rocco, due to punishment, with the yellow-blacks coming into the game again offensively and taking the lead thanks to the goal of Savevski.

At Nikos Goumas Stadium, the yellow-blacks entered the match offensively, but in the 21st minute, the referee did not whistle Loko's foul on Vlachos and the Frenchman was left unmarked and scored.

Their next opponent were Sturm Graz, where the yellow-blacks won with 2–0 at home with Marcelo and Batista, but at the expense of the serious injury of Christos Kostis, after a collision with Kazimierz Sidorczuk, effectively ending his career that night, as he never managed to return.

Nevertheless, AEK pulled off a reaction in the stoppage time and responded with two goals by Nikolaidis and Sebwe that allowed them not only to avoid humiliation, but also claiming the chances of qualifying in the rematch.

In Nea Filadelfeia, AEK, led by Nikolaidis, who achieved a quick hat-trick, made the game take on a procedural nature and after the qualification was decided, the Greek side scored a fourth goal with Donis.

In the second leg at Råsunda Stadium, AEK were more offensive, but an inactivity of Ilias Atmatsidis, costed them the presence in the group stage, as they conceded a goal by Nebojša Novaković, which made the final 1–0.

The rematch of Nikos Goumas was an even more impressive night for AEK, who scored at the beginning of the match with Navas, while in the second half they doubled their lead with a direct free kick from Tsiartas and achieved a huge qualification win.

A 4–0 win with goals by Grigoris Georgatos, Demis Nikolaidis, Milen Petkov and Theodoros Zagorakis and the a 1–4 in Nicosia with the braces of Vasilios Lakis and Kostas Katsouranis and another by Dimitris Nalitzis.

AEK's undefeated run was brought to an end in the round of 16 by Málaga, even though they drew 0–0 at La Rosaleda Stadium, lost by 0–1 at Nea Filadelfeia with a goal from Manu.

Next game against Eindhoven at Philips Stadium, AEK appeared again in a tragic situation and conceded 2 goals by Bouma and Robben and with the final 2–0 defeat were essentially out of the Champions League.

There, in a relatively difficult draw, they found themselves in the same group as Sevilla, Lille, Zenit Saint Petersburg and Alemannia Aachen, where they had a very bad campaign with 4 defeats in equal matches, thus stayed out of the continuation of the tournament.

In an electrified atmosphere and with an excellent appearance, AEK got the huge win by 1–0 with a free-kick by Júlio César, while Stefano Sorrentino with an amazing performance kept the clean seat.

[10] In the game, AEK put a lot of pressure on Sevilla, eventually conceded 4 goals Fabiano, Keita and Kerzhakov, only to reduce with Rivaldo in the heavy 1–4 defeat and continued in the UEFA Cup.

In Athens, Getafe took the lead with Rubén de la Red with AEK closing the Spaniards in their area, reaching an equalizer with a back-heel goal from Ismael Blanco.

In the rematch at the Olympic Stadium, AEK in one of their best European appearances in recent years turned the qualifying event into a triumph, by winning by 3–0 with a goal by Christodoulopoulos and two more by Simões, dominating their opponents throughout the match.

In the first matchday at Stadion Rujevica, the yellow-blacks took the lead early on with Mantalos, but in the only chance found in the game Rijeka equalized with Elez only for Christodoulopoulos to form the final 1–2 win with a free-kick.

The final whistle found AEK in the Champions' League group stage and Livaja receiving an unacceptable red card for attacking an opponent player, as well as a 4-match ban.

The crushing failure in the match combined with the second consecutive home defeat in the league, resulted in the sacking the manager Miguel Cardoso, who was replaced by Nikos Kostenoglou.

The first leg took place at Stadion Grbavica, AEK entered the match well and managed to take an early lead with Ansarifard, but a mistake by Tsintotas brought the quick equalization for Velež.