Boëtius made his debut for Feyenoord at the age of 18, when then-manager Ronald Koeman named him in the starting line-up in De Klassieker, the main football rivalry in The Netherlands, at home against long-time rivals Ajax on 28 October 2012. Having never made the bench before, Boëtius was a shock addition in the starting line-up and ended up scoring the equaliser in a game that ended in a 2–2 draw to cap off a positive debut performance. He quickly became a starter for the Rotterdam-based club as a left winger. In his first season in the Eredivisie, Boëtius played in 20 league games, scoring 4 goals and delivering 2 assists. Feyenoord finished the 2012–13 season on 3rd position and secured a spot in the Europa League play-off’s for the next season. However, Boëtius’ season was ended prematurely after suffering a knee injury during a training session in April.

Because of the knee injury, Boëtius missed the beginning of the 2013–14 season. He made his season debut on 15 September 2013 coming off the bench in the 62nd minute against NEC Nijmegen. Just five minutes after entering the pitch Boëtius scored a goal giving his team a 2–1 lead. During the season Boëtius scored 10 goals in 29 appearances. He finished 3rd among the league’s assists leaders with a total of 9 assists. Feyenoord ended the season on the second place only behind Ajax, earning a spot in the UEFA Champions League third qualifying round.

On 6 March 2013, Boëtius was called up for the preliminary squad of the Dutch national team for the first time, aged only 18. He made his debut for the Netherlands national team on 5 March 2014 in an exhibition match against France at Stade de France in Saint-Denis. He started the match as a left winger but was substituted in the 72nd minute as the Netherlands were defeated 0–2.

On 2 August 2015, it was announced that Boëtius was signed by Swiss side Basel. He made his first team debut for Basel in the 2015–16 UEFA Champions League play-off round on 19 August in the match against Maccabi Tel Aviv which ended in a 2–2 draw. He gave his 2015–16 Swiss Super League debut on 22 August in the 3–1 away win against FC Lugano. Under trainer Urs Fischer Boëtius won the Swiss Super League championship at the end of the season. For the club it was the seventh title in a row and their 19th championship title in total. On 31 January 2017, Boëtius was loaned to Belgian club K.R.C. Genk for the remainder of the season.

On 23 June 2017, Feyenoord announced that Boëtius would return to the club on a three-year contract. On 22 April 2018, he played as Feyenoord won the 2017–18 KNVB Cup final 3–0 against AZ Alkmaar.

In August 2018, Boëtius joined Bundesliga side 1. FSV Mainz 05 on a four-year contract. The transfer fee paid to Feyenoord was reported as €3.5 million.

On 20 June 2020, Boëtius scored Mainz’s second goal in a 3–1 victory over Werder Bremen in the penultimate match of the Bundesliga season. The win secured the club’s place in the Bundesliga for the following campaign.