The former France international, who won five major honours in total including a treble in his second and final campaign, is said to have departed by “mutual agreement”.
Pedros, who took charge in 2017, took the club to a league and European double in his maiden season, before repeating the feat with the addition of the Coupe de France.
The one-time European Championship semi-finalist was named FIFA’s Women Coach of the Year for his efforts in 2018.
With little else to achieve however, both Pedros and Lyon “felt that it was necessary to change the technical organization in order to stimulate a new dynamic,” the latter confirmed in an official statement .
“Olympique Lyonnais and its President Jean-Michel Aulas thank Reynald Pedros for his investment and the quality of his work throughout these two seasons of total collaboration that allowed the club, its women's team and the players to win five new trophies.
“Jean-Michel Aulas wishes Reynald Pedros great success for the rest of his career and will keep fond memories of their collaboration.
“[It] was marked by a great openness between both sides and culminated with a Treble winning 2018/19 season that helped the development of women’s football in France.”
Since his arrival, Pedros has helped to further Lyon’s domination of the women’s game in Europe, with the club having competed in eight Champions League finals since 2010, winning six.
They have also been Division 1 Feminine winners in every season since 2006-07, and have counted several of the world’s greatest players among their ranks, including incumbent Ballon d'Or Feminin holder Ada Hegerberg.
14 of their players are on duty alone at the current World Cup in France, though England’s Izzy Christiansen is one player from the club who didn’t make the cut for the tournament.
Lyon will now begin their search for a new head coach as they look to extend their domestic dominance of the game across the continent and defend their titles.