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The club was founded in 2011, as a result of a merger between BV Lely and Mosquitos, both clubs from Amsterdam. Its name is derived from its home venue the Apollohal. Apollo took over the license of the old ABC Amsterdam second team. In the first season of the club, Apollo played as an amateur team in the Promotiedivisie. They immediately won the Dutch amateur championship after defeating CBV Binnenland in the league final.

In 2012, Apollo club decided to enter the professional Dutch Basketball League (DBL) for the 2012–13 season. In its first season, led by coach Tyrone Marioneaux and All-Star Aron Royé, Apollo finished in ninth place in the DBL.

In 2013–14, Apollo managed to reach the playoffs for the first time in franchise history. The club lost in the quarterfinals to GasTerra Flames, 0–2.

During Apollo's most successful season since their establishment, the club had financial problems which made it close to withdrawing from the DBL. However, in August 2014 it was announced Apollo would continue playing in the DBL.

In the 2015–16 season, Apollo made its second appearance in the DBL playoffs where it lost to Den Bosch 0–2 in the quarterfinals.

Apollo won its first playoff game in 2016, defeating ZZ Leiden in Game 1 of the quarterfinals. However, in a packed Apollohal, Leiden retrieved home advantage and went on to beat Apollo 1–2 and advance to the semifinals.

On 1 May 2020, Apollo announced it will not play in the 2020–21 DBL season because of uncertainty caused by the COVID-19 pandemic. Apollo also announced Laki Lakner was replacing Patrick Faijdherbe as head coach. Lakner resigned after three games, and Edwin van der Hart took over for the remainder of the season. Apollo finished in ninth place for a second season in a row.

Since the 2021–22 season, Apollo plays in the BNXT League, in which the national leagues of Belgium and the Netherlands have been merged. In June 2021, Wierd Goedee was signed as new head coach.

In June 2023, following the 2022–23 season, Apollo was forced to withdraw from the BNXT League as it was unable to come up with the necessary budget for participation. The BNXT organisation required a minimum budget of €350,000 which Apollo was unable to bring together with its sponsorships. Apollo entered the second-level Promotiedivisie for the 2023–24 season.