Club career
Valencia
Lee joined Valencia's academy in July 2011. On 15 December 2017, he was called up to Valencia B (Mestalla). He had his debut on 21 December 2017, in a match with Deportivo Aragón, being substituted in the 82nd minute.
Lee made his first team debut on 30 October 2018, starting and playing 83 minutes in a 2–1 win over Ebro in the Copa del Rey, becoming the youngest South Korean footballer to debut professionally in Europe.
Lee made his La Liga debut on 12 January 2019, substituting in for Denis Cheryshev in the 86th minute in a 1–1 draw with Real Valladolid during 2018–19 season. At 17 years, 10 months, and 24 days, Lee became the second youngest player in the 18–19 La Liga after Ander Barrenetxea from Real Sociedad who debuted at the age of 16 years, 11 months, and 24 days. He also became the youngest ever non-Spanish and the first Asian league debutant for Valencia, as well as the fifth Korean to play in La Liga.
On 30 January 2019, Lee officially joined the Valencia first-team, receiving jersey number 16.
On 17 September 2019, Lee made his UEFA Champions League debut as a late substitute for Rodrigo in a 1–0 win against Chelsea, becoming the youngest ever Korean to debut in the competition at the age of 18 years and 6 months, a record previously held by Jeong Woo-yeong. He also became the 5th youngest ever to debut for Los Ches in the same competition. On 25 September 2019, he scored his first La Liga goal in a 3–3 draw against Getafe, to become the youngest non-Spanish to score for Valencia, aged 18 years and 219 days old, breaking the previous record of Mohamed Sissoko who scored in the 2003–04 UEFA Cup; and the third youngest ever, only behind Juan Mena and Fernando Gómez. His record as the youngest non-Spanish goalscorer for Valencia was broken the following season by American teammate Yunus Musah.
On 13 September 2020, Lee became the youngest player, aged 19 years and 207 days, to assist two goals in a La Liga match in the 21st century, in a 4–2 win over Levante, breaking the previous record of Juan Mata in 2008, aged 20 years and 150 days. Despite rejecting several renewal offers from the club throughout the year, he featured regularly under Javi Gracia as the Che ended the campaign on a mid-table position.
After being on the transfer list during the entire pre-season, Lee terminated his contract with Valencia on 29 August 2021.
Mallorca
On 21 August 2021, fellow La Liga club Mallorca confirmed the free transfer of Lee, signing on a four-year contract.
During the 2022–23 season, Lee became one of the best dribblers in the Big Five European leagues, with the highest dribble success rate and the sixth-highest number of successful dribbles.
Paris Saint-Germain
On 8 July 2023, Ligue 1 club Paris Saint-Germain announced the signing of Lee on a five-year contract running through 2028, becoming the first ever South Korean to play for the club. A transfer fee of €22 million was paid out to Mallorca after Lee passed his medical at the start of June.
On 12 August, he made his Ligue 1 debut in a 0–0 draw against Lorient at the Parc des Princes. On 25 October, he scored his first PSG goal and his first Champions League goal in a 3–0 victory over AC Milan. On 3 November, he scored his first Ligue 1 goal in a 3–0 win over Montpellier. On 3 January 2024, he was named man of the match, after he scored the opening goal in the 2–0 Trophée des Champions win over Toulouse, where he won his first title with the club. As PSG won the Double of the Ligue 1 and the Coupe de France in the 2023–24 season, he became the first Asian player to win the Ligue 1.
In the 2024–25 season, Lee became the second Asian ever to receive a UEFA Champions League medal, following compatriot Park Ji-sung, but his playing time during the second half of the season decreased sharply due to Khvicha Kvaratskhelia's arrival and Désiré Doué's growth. He considered his transfer in the summer despite winning a continental treble, whereas the club was less willing to sell him actively. On 15 June 2025, he came on as a 72nd-minute substitute and scored his first FIFA Club World Cup goal on a penalty kick in a 4–0 win over Atlético Madrid.
At the 2025 UEFA Super Cup on 13 August, Lee was put into the field in the 67th minute when Tottenham Hotspur held a 2–0 lead. He scored PSG's first goal, which underlay a 2–2 tie, and their third penalty goal in a 4–3 penalty shoot-out win. During the 2025–26 season, he still remained a back-up for PSG as they secured their second successive Champions League title. While PSG's main players concentrated on winning the Champions League, he helped the club win their 12th Ligue 1 title in 14 years. On 30 May 2026, he became the first ever Asian to lift multiple UEFA Champions League trophies when his teammates defeated Arsenal on penalties in the final.
Atlético Madrid
On 25 July 2026, Lee signed a five-year contract with Atlético Madrid till June 2031. The deal was worth approximately €40 million, with €35 million fixed plus €5 million in add-ons. In his first competitive game for Atlético against Málaga, he scored the opening goal and was the match's MVP; his goal would go on to win La Liga Goal of the Month for August 2026. Less than a month later, he won the MVP award again after a dominant performance against Osasuna.

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La Liga
Champions League