"The club and its coach felt that it was necessary to change the technical organisation to stimulate a new dynamic and that different methods and approach allow the women's team to regenerate and continue to progress," the club said in a statement.
Pedros, a former midfielder, was named the best women's coach in the world by FIFA last year for his achievements at Lyon.
His final match in charge was the 4-1 win over Barcelona in Budapest last month to clinch the club's record sixth Champions League title.
Lyon, regarded by many as the greatest club side in women's football, have also won a record 17 league titles and 10 French Cups. A number of their players are involved in the women's World Cup which is being hosted in France until July 7.
(Reporting by Christian Radnedge; Editing by Toby Davis)
