It is not clear whether the amount of accumulated lactate is the main factor limiting muscle glycogen accumulation during recovery from an intense sprint performed by previously active fasted laboratory rats. To address this question, groups of fasted rats swam at moderate intensity for 30 min, each animal with a lead weight equivalent to 0.5% body mass attached to its tail, followed by a 3 min high intensity swim with a 10% lead weight and a recovery period of up to 2 hours afterwards. Moderately intense exercise for 30 min caused a decrease in muscle glycogen levels in the mixed, white and red gastrocnemius and the mixed quadriceps muscles, and a further rapid fall occurred in response to the 3 min sprint effort. During recovery, glycogen increased to comparable or above pre-sprint levels across all muscles, and this occurred to a large extent at the expense of net carbon sources other than lactate, with these carbon sources accounting for at least 36–65% of the glycogen deposited. The sustained dephosphorylation-mediated activation of glycogen synthase, but not the changes in glucose 6-phosphate levels, most probably played an important role in enabling the replenishment of muscle glycogen stores. In conclusion, our findings suggest that the amount of glycogen deposited during recovery from high intensity exercise in fasted animals is not limited by the amount of accumulated lactate.