Fekir was included in the Lyon first team squad for the first time on 30 July 2013, remaining as an unused substitute in 1–0 home win over Grasshopper in the Champions League third qualifying round first leg.
He finally made his Lyon first team debut on 28 August 2013, replacing Yassine Benzia at half time in a 2–0 Champions League play-off round second leg away loss to Real Sociedad, which saw the club eliminated from the tournament after a 4–0 aggregate defeat.
Three days later he made his Ligue 1 debut, playing the entire match in 2–1 away defeat to Evian TG.
On 27 April 2014, against Bastia in a 4–1 Ligue 1 home win, he scored his first competitive goal (in the 23rd minute) for Lyon's first team and assisted one goal each for Bakary Koné and Alexandre Lacazette.
Fekir made a total of 17 appearances in all competitions in his first season (2013–14) with Lyon's first team, scoring one goal.

During the 2014–15 season, he featured regularly for the first team and by 19 March 2015 he had scored 11 goals and assisted 7 in 25 2014–15  season Ligue 1 games, earning him his first international call up.
On 17 May 2015, he was named as the Ligue 1 Young Player of the Year and earned a spot in the Team of the Year.
He finished the 2014-15 Ligue 1 season with 13 goals and 9 assists.

On 29 August 2015, Fekir scored a hat-trick in a 4–0 Ligue 1 away win at Caen.
He missed most of the 2015–16 season with torn knee ligaments.

On 23 February 2017, Fekir scored a hat-trick and assisted Mouctar Diakhaby's 89th-minute goal) in the 2016-17 Europa League round of 32 second-leg 7–1 home win over AZ Alkmaar to be on the scoresheet of a UEFA Europa League or UEFA Champions League match for the first time in his career, by 23 February he had scored 10 goals and provided 10 assists in all competitions for the 2016–17 season.

In early August 2017, following the transfer of Maxime Gonalons to AS Roma a month earlier, Fekir was named captain of the club.
On 5 November, he scored two goals in a 5–0 away Ligue 1 victory over fierce rivals AS Saint-Etienne.
 After Fekir scored his second goal in the 84th minute, he took off his shirt and brandished his name and number to the Saint-Étienne supporters, who threw objects and spilled onto the field, outraged by the gesture.
Referee Clément Turpin led the players away from the field and riot police ran onto the field to restore order.
The match was stopped for 40 minutes before the two teams could play out its final five minutes in a virtually empty Stade Geoffroy-Guichard.

In 2017–18, Fekir was part of a prolific forward line alongside Memphis Depay and Mariano; he contributed 18 goals, the Dutchman contributing 19, with the Spaniard totalling 18 for the team.

In June 2018, Liverpool negotiated with Lyon for the transfer of Fekir, offering a maximum €60 million but were not successful.
Fekir was included in the Lyon first team squad for the first time on 30 July 2013, remaining as an unused substitute in 1–0 home win over Grasshopper in the Champions League third qualifying round first leg. He finally made his Lyon first team debut on 28 August 2013, replacing Yassine Benzia at half time in a 2–0 Champions League play-off round second leg away loss to Real Sociedad, which saw the club eliminated from the tournament after a 4–0 aggregate defeat. Three days later he made his Ligue 1 debut, playing the entire match in 2–1 away defeat to Evian TG. On 27 April 2014, against Bastia in a 4–1 Ligue 1 home win, he scored his first competitive goal (in the 23rd minute) for Lyon's first team and assisted one goal each for Bakary Koné and Alexandre Lacazette. Fekir made a total of 17 appearances in all competitions in his first season (2013–14) with Lyon's first team, scoring one goal.
During the 2014–15 season, he featured regularly for the first team and by 19 March 2015 he had scored 11 goals and assisted 7 in 25 2014–15  season Ligue 1 games, earning him his first international call up. On 17 May 2015, he was named as the Ligue 1 Young Player of the Year and earned a spot in the Team of the Year. He finished the 2014-15 Ligue 1 season with 13 goals and 9 assists.
On 29 August 2015, Fekir scored a hat-trick in a 4–0 Ligue 1 away win at Caen. He missed most of the 2015–16 season with torn knee ligaments.
On 23 February 2017, Fekir scored a hat-trick and assisted Mouctar Diakhaby's 89th-minute goal) in the 2016-17 Europa League round of 32 second-leg 7–1 home win over AZ Alkmaar to be on the scoresheet of a UEFA Europa League or UEFA Champions League match for the first time in his career, by 23 February he had scored 10 goals and provided 10 assists in all competitions for the 2016–17 season.
In early August 2017, following the transfer of Maxime Gonalons to AS Roma a month earlier, Fekir was named captain of the club. On 5 November, he scored two goals in a 5–0 away Ligue 1 victory over fierce rivals AS Saint-Etienne.  After Fekir scored his second goal in the 84th minute, he took off his shirt and brandished his name and number to the Saint-Étienne supporters, who threw objects and spilled onto the field, outraged by the gesture. Referee Clément Turpin led the players away from the field and riot police ran onto the field to restore order. The match was stopped for 40 minutes before the two teams could play out its final five minutes in a virtually empty Stade Geoffroy-Guichard.
In 2017–18, Fekir was part of a prolific forward line alongside Memphis Depay and Mariano; he contributed 18 goals, the Dutchman contributing 19, with the Spaniard totalling 18 for the team.
In June 2018, Liverpool negotiated with Lyon for the transfer of Fekir, offering a maximum €60 million but were not successful.
Nabil Fekir