Jørgensen joined F.C. Copenhagen from Herfølge Boldklub as a youngster. Here he played in various Copenhagen youth teams and did so well that 17-year-old Jørgensen signed a new three-year contract in December 2022.[1] In May 2023 Jørgensen was included in the first team squad for the first time when he was selected for a Danish Superliga match against AGF. However, it did not turn into a debut.[2]
Still with his professional debut still to come, Jørgensen was loaned out to Hvidovre IF at the end of January 2024 until the end of the season.[3] During his loan spell, 18-year-old Jørgensen played every game for Hvidovre, the majority of which were starts. Jørgensen was named Young Player of the Month in the Danish Superliga in March 2024.[4] However, Hvidovre were relegated to the Danish 1st Division and Jørgensen returned to Copenhagen in the summer of 2024.[5]
On 20 August 2024, Viborg confirmed that they had signed Jørgensen on a deal until the summer of 2028[6] for a reported fee of 4.5 million kr.[7] He made his debut for the club six days later on 26 August in a 1–0 home victory for Viborg over Lyngby.[8]