Koo started football at age ten when a nearby elementary school opened its football club. During his early youth career, he mostly played as a defender, often taking sweeper role. However, he wasn’t particularly outstanding and the fact he suffered from anemia also hindered him from gaining attention. In 2006, as a member of Boin High School, Koo participated in the Baekrok High School Football Competition that is annually held in Jeju Island. Leading Boin High School to a runner-up place with an outstanding performance, he grabbed the attention of Jung Hae-seong, who was then the manager of Jeju United.

In 2007, Koo was selected by Jeju United in the K League draft. He failed to make an impression in his first two years at Jeju due to numerous injuries. However, he slowly broke into the first team, mostly playing as a defensive midfielder. In January 2010, he was reportedly invited by Blackburn Rovers for a trial, but the move didn’t happen. He spent a great season in 2010 at Jeju instead, driving his club to an unprecedented runner-up position. His contribution also enabled him to gain personal honors, as he received the FANtastic Player award and the Top Assists Award and was included in the K League Best XI.

On 30 January 2011, Koo Ja-cheol successfully moved to VfL Wolfsburg during the winter transfer window, signing a three-and-a-half year contract for an undisclosed fee. On 12 February 2011, Koo made his Wolfsburg debut against Hamburger SV, coming on as a substitute in the 64th minute in the 1–0 home defeat. However, he had difficulty competing for places in the starting line-up during a year.

Koo played a central role in helping South Korea finish third in the 2011 AFC Asian Cup, with five goals and three assists over the tournament, finishing as the tournament’s top scorer.

On 31 January 2012, he moved on loan to the league rivals FC Augsburg. On 18 February 2012, he scored the equalizer with a non-stop curve shot outside the penalty area but his team lost 4–1 against Bayer Leverkusen. On 17 March 2012, he scored the equalizer with a lob outside the penalty area and contributed to a 2–1 victory against Mainz 05. On 24 March 2012, he assisted the equalizer and his team drew 1–1 with Werder Bremen. On 31 March 2012, he scored the opening goal with a low shot outside the penalty area and contributed to a 2–1 victory against 1. FC Köln. On 7 April 2012, he scored the equalizer through Manuel Neuer’s legs, but his team lost to Bayern Munich 2–1. On 5 May 2012, he scored the winning goal with a header and led a 1–0 victory against Hamburger SV. During the loan period, he recorded five goals and two assists in 15 appearances, and became the top scorer of his team, although only played half of the season. He performed a significant part in helping Augsburg escape relegation in their maiden season in the Bundesliga.

In his second season at Augsburg, Koo was plagued by injuries but still helped the club survive relegation in the limited games he played in. In December 2012 he was involved in an on the field altercation with Bayern Munich’s midfielder Franck Ribéry in the 2012–13 DFB-Pokal. After a disputed free kick he confronted Ribéry and touched his face, in response Ribéry slapped Koo. Referee Thorsten Kinhöfer gave Koo a yellow card and sent off Ribéry. Bayern Munich director Karl-Heinz Rummenigge demanded that the ejection be overturned, while Bayern’s coach Jupp Heynckes blamed both Koo and Ribéry, stating that although Koo had provoked Ribéry the latter should learn to not react under pressure.

During the 2012 Summer Olympics, Koo played as a central midfielder in the South Korea under-23 team. He appeared in every game in the tournament, and scored the second goal during the second half of the bronze medal match against Japan, securing a 2–0 victory for Korea. The South Korean team won the bronze medal in football for the first time in its Olympics history and in doing so, became the second Asian team in the Olympics men’s football to reach the semi-finals.

Koo likes to go shopping in his spare time in Germany. He is currently the honorary ambassador for The Republic of Korea Air Force. Koo is also a close friend with his teammate Ki Sung-yueng, and they like to display their friendly, humorous conversations on Twitter. Ki revealed on the Korean talk show Healing Camp, Aren’t You Happy that Koo has a nickname called “Koogle Georim” (Korean: 구글거림) because of his sometimes goofy way of talking. On 24 June 2013, Koo married a Jeju woman three years his senior at the Sheraton Grande Walkerhill Hotel.

In the 2013–14 season, he returned to Wolfsburg and was deployed as a central midfielder or winger, but he wanted more appearances and preferred playing as an attacking midfielder like when he played for Augsburg. On 18 January 2014, it was announced that Koo penned a four-and-a-half year deal with Mainz 05. On 1 February 2014, he scored his first goal for Mainz in a 2–0 victory over SC Freiburg. In the 2014–15 season, however, he was used as a winger to substitute Eric Maxim Choupo-Moting and Nicolai Müller who had left Mainz 05. On 31 July 2014, he contributed to a 1–0 victory by assisting the winning goal against Asteras Tripoli in the third qualifying round of the 2014–15 UEFA Europa League. On 7 August 2014, he scored a goal, his first in the UEFA competition, but his team lost 3–1 to Asteras Tripoli in the second leg and was eliminated from the tournament. On 15 August 2014, he scored a goal, but his team didn’t finish the game during 120 minutes by drawing 5–5 with a third division club Chemnitzer after extra time in the first round of the 2014–15 DFB-Pokal. In the penalty shoot-out, he scored the second goal of team, but they lost 5–4 and experienced a shock. He recorded five goals and two assists with 23 appearances in the 2014–15 Bundesliga.

On 31 August 2015, Koo rejoined Augsburg, so Augsburg played a season with three South Korean players, including Ji Dong-won and Hong Jeong-ho. On 12 September 2015, he assisted the opening goal with a backheel pass in the first half, but his team lost 2–1 to Bayern Munich by conceding two goals in the second half. On 23 September 2015, he brought a penalty kick against Granit Xhaka, but they lost 4–2 to Borussia Mönchengladbach. On 21 February 2016, he broke through the left of Hannover 96 alone with his dribbling and scored the winning goal. On 6 March 2016, he scored the first hat-trick of Augsburg in the Bundesliga, but Augsburg didn’t protect their 3–0 lead and drew 3–3 with Bayer Leverkusen. He recorded eight goals and four assists with 29 appearances in the 2015–16 Bundesliga. He also participated in the 2015–16 UEFA Europa League, the first UEFA competition of Augsburg. They recorded three wins and three losses in the group stage, and succeeded in advancing to the knockout stage, but lost 1–0 on aggregate to Liverpool in the round of 32. After the 2015–16 season, he was ranked fifth of attacking midfielder side in the player rankings of kicker.

On 25 January 2019, Koo announced his retirement from international duty after South Korea lost in the quarter-finals of the 2019 AFC Asian Cup.

On 3 February 2020, he achieved his 200th Bundesliga appearance against Mainz 05. He left Augsburg by turning down an extension offer from the club after the 2018–19 season. He wanted to contract with high ranking clubs of the Bundesliga, but finally joined Qatar Stars League side Al-Gharafa in August 2019.