Junker started playing football as a four-year-old with local club Vinding SF before moving to the Vejle Boldklub academy and from there on to Kolding IF. He joined Hessel Gods Fodboldkostskole (Hessel Gods Football Academy) in tenth grade, where he was coached by the likes of Flemming Povlsen and played for FC Djursland's team in the Denmark Series.[3] Junker was spotted by scouts of Randers, whom he joined at U19 level in the summer of 2012, while attending HHX ("Higher Commercial Examination Programme") at Tradium Randers.[4]
Randers
Junker made his Danish Superliga debut for Randers as a substitute in the away match against Vestsjælland on 7 March 2014, and contributed with an assist to Kasper Fisker's goal in the 1–1 draw.[5] Junker also came on the pitch on 4 April when Randers beat AGF 1–0 in Aarhus.[6]
In the summer of 2014, he signed a full-time contract with Randers, and was thus promoted to the first team and became a professional.[7] In January 2015, he was sent on a six-month loan to second-tier Danish 1st Division club Fredericia, but failed to make an appearance.[8]
AGF
In the summer of 2016, Junker signed a three-year contract with Randers' Superliga rivals to the south, AGF,[9] where he began the season as a starter due to Morten "Duncan" Rasmussen's injury in a pre-season match.[10]
Horsens
On the last day of the transfer window, 31 August 2018, Junker signed with AC Horsens on a five-year contract for an undisclosed fee. However, the Horsens stated that it was a record transfer fee for the club.[11]
Norway
On 9 August 2019, Junker was loaned out to Norwegian club Stabæk from Horsens for the rest of 2019 with an option to buy.[12] On 17 December 2019, he signed a three-year contract with Norwegian club Bodø/Glimt from 1 January 2020.[13]
Japan
In April 2021 he was sold to Japanese club Urawa Red Diamonds.[14] On 5 January 2023, Nagoya Grampus announced the signing of Junker on loan from Urawa Red Diamonds for the season.[15] On 5 January 2023, fellow J1 League club Nagoya Grampus announced the signing of Junker on loan for the 2023 season.[16] At the end of the campaign, he left Urawa following the expiration of his contract, and subsequently joined Nagoya Grampus on a free transfer for the 2024 season.[17][18]