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Morocco's first appearance was in the 1964 Summer Olympics in Tokyo. In a group that consisted of three teams following North Korea's withdrawal. They suffered a heavy 0-6 defeat to Hungary - Morocco's all-time heaviest defeat to date -, then lost 1-3 to Yugoslavia and were eliminated.

Their second appearance was supposed to be during the 1968 Summer Olympics in Mexico but Morocco refused to allow its team to play against Israel in Group C due to political issues. They were eventually replaced by Ghana which lost 2-3 on aggregate to Morocco in the last qualifying round.

In the 1972 edition in Munich, Morocco reached the second round as runners-up in their group with 3 points following a goalless draw against the United States, a resounding 6-0 win against Malaysia and a 0-3 loss to hosts West Germany. In the second round, The Atlas Lions lost all three games against Denmark, Poland and the Soviet Union. However, it remains the best performance of the Atlas Lions at the Olympic football tournament to date.

Morocco came extremely close to reaching the quarter-finals in the 2004 Summer Olympics, narrowly missing out on goals scored that favored Costa Rica. Morocco were 2-1 ahead in their final group game against already-qualified Iraq thanks to goals scored by Bouabid Bouden and Salaheddine Aqqal. However, in the other game, Costa Rica's Pablo Brenes scored the fourth goal in added time to seal a 4-2 win over Portugal and qualification at Morocco's expense.

During the inaugural 2011 CAF U-23 Championship held in Morocco. The host nation coached by Pim Verbeek, recorded narrow victories against heavy favourites Nigeria and Algeria before losing to Senegal. In the semi-finals, Morocco successfully secured a spot in the 2012 Summer Olympics in London by defeating Egypt 3-2 in a tense game which also saw Abdelaziz Barrada scoring the fastest goal in the history of the tournament (as of 2023) after 30 seconds. This marked the return of the Atlas Lions to the Olympic football tournament having missed out on qualifying in 2008. However, they faced a setback when they suffered a 2-1 defeat against the surprising contender, Gabon, in the final held at the Marrakech Stadium.

First continental title

On 7 July 2022, Morocco were awarded the hosting rights of the 2023 U-23 Africa Cup of Nations, marking the return of the U-23 team to the competition for the first time in 12 years. Their campaign kicked off on a positive note with a hard-fought 2-1 victory against Guinea, followed by a resounding 5-1 triumph over Ghana, emerging as group winners and securing a place in the semifinals with one game to spare. They went on to win the semi-final against Mali and qualify for the 2024 Olympic Games. They defeated Egypt 2-1 in the final to win their first ever continental title. The team was congratulated by King Mohammed VI for their achievement.

On 29 February 2024, Tarik Sektioui was appointed head coach of the men's Olympic squad by the Royal Moroccan Football Federation.