The club's "important defeat Saturday against Troyes, which kept it from accessing the Champion's League, was certainly behind the Lens coach's decision," the club said on its Web site.
Troyes beat Lens 3-0 on Saturday, the final day of French League play, dropping Lens from third place and the final qualifying berth to fifth.
Gillot, a former defender with the club Sang et Or, took over at Lens in January 2005. Under his leadership, the team placed seventh, fourth and fifth in the French League over the past three years.
Gillot's replacement was not announced.