Growing up in Hjerk, Salling, Isaksen moved to the Midtjylland academy from Roslev IK at under-12-level, after having started playing football as a three-year-old.
[3] After he signed his first professional contract in May 2019 – a five-year deal –[4] he made his debut on 25 August 2019 in the Danish Superliga when he came on as a substitute for Awer Mabil in the 78th minute of the 2–0 away win over SønderjyskE.
[1] On 25 November 2020, Isaksen made his first European appearance, coming on as a substitute for Anders Dreyer in the 82nd minute of a 3–1 loss to Ajax in the UEFA Champions League group stage.
[8] On 20 February 2023, Isaksen scored his first hat-trick in Midtjylland's spring opener against Viborg, which ended in a 4–0 victory.
On 4 September 2020, he made his Denmark under-21 debut in a 1–1 draw against Ukraine, coming on as a substitute for Rasmus Carstensen in the 81st minute.