Following his first-team debut with SC Heerenveen, Ilsø never managed to make another senior team appearance for the rest of his time at the club.

Unable to break into the first-team plans of SC Heerenveen, Ilsø returned in 2007 to Denmark, and joined local club SønderjyskE.

[15] On 15 December 2012, in a Bundesliga match against Hannover 96, Ilsø played an integral role by scoring the decisive goal for Fortuna Düsseldorf to end the tie in a 2–1 victory.

In February 2014, Ilsø joined Chinese Super League side Guangzhou R&F, but he left the club after only three months due to a reduction in his playing time.

[22] Ilsø notched his 4th of the season in his 4th consecutive league match for Home United, scoring the first goal of a 2–2 draw against Brunei DPMM.

[24] Home United coach, Philippe Aw, was chosen to manage the Singapore Selection side for the 2016 Sultan of Selangor Cup.

[28] Following speculation after his rejection of a contract renewal with Home United, Ilsø was confirmed to be on trial with the 2016 Malaysia Cup champions, Kedah FA, on 27 December 2016.

[29] It was later officially announced on 3 January 2017 that Ilsø had signed a one-year contract with the club to play for the entirety of the 2017 Malaysia Super League season, after impressing head coach Tan Cheng Hoe during the trial.

[30] Ilsø joins Kedah FA as the club's third foreign signing, linking up with Liridon Krasniqi of Kosovo, and Sandro da Silva Mendonça of Brazil.

[35] Ilsø made his debut in a friendly match against National Premier League side Para Hills Knights where he earned an assist in a 2–0 victory on 10 July 2018.