Activation of autophagy in skeletal muscle has been reported in response to endurance exercise and food deprivation, independently. The purpose of this study was to evaluate whether autophagy was more activated when both stimuli were combined, namely when endurance exercise was performed in a fasted rather than a fed state. Mice performed a low intensity running exercise (10m/min for 90min) in both dietary states after which the gastrocnemius muscles were removed. LC3b-II, a marker of autophagosome presence, increased in both conditions, but the increase was higher in the fasted state. Other protein markers of autophagy like Gabarapl1-II and Atg12 conjugated form as well as mRNA of Lc3b, Gabarapl1 and p62/Sqstm1 were only increased when exercise was performed in a fasted state. The larger activation of autophagy by exercise in a fasted state was associated with a larger decrease in plasma insulin and phosphorylation of Akt^Ser473, Akt^Thr308, FoxO3a^Thr32 and ULK1^Ser757. AMPKα^Thr172, ULK1^Ser317 and ULK1^Ser555 remained unchanged in both conditions whereas p38^Thr180Tyr182 increased during exercise to a similar extent in the fasted and fed conditions. The marker of mitochondrial fission DRP1^Ser616 was increased by exercise, independently of the nutritional status. Changes in mitophagy markers BNIP3 and Parkin suggest that mitophagy was increased during exercise in the fasted state. In conclusion, our results highlight a major implication of the insulin/Akt/mTOR pathway and its downstream targets FoxO3a and ULK1 in the larger activation of autophagy observed when exercise is performed in a fasted state, as compared to a fed state.