We sought to determine whether lipolysis, fatty acid (FA) mobilisation, and plasma FA oxidation would remain elevated for hours following isoenergetic exercise bouts of different intensities. Ten men and eight women received a primed-continuous infusion of [1,1,2,3,3-2H5]glycerol and continuous infusion of [1-13C]palmitate to measure glycerol and plasma FFA kinetics. On Day 1 (D1), participants were studied under one of 3 different conditions, assigned in random order: (1) before, during and 3 h after 90 min of exercise at 45% V·O2peak (E45), (2) before, during and 3 h after 60 min of exercise at 65% V·O2peak (E65), and (3) in a time-matched sedentary control trial (C). For each condition, participants were studied by indirect calorimetry the following morning as well (D2). Rate of appearance (Ra) of glycerol (RaGL) increased above C during exercise in men and women (p < 0.05), was higher in E45 than E65 in men (P < 0.05), and was not different between exercise intensities in women. During 3 h of post-exercise recovery, RaGL remained significantly elevated in men (P < 0.05), but not women. FA Ra (RaFA) increased during exercise in men and women and was higher in E45 than E65 (P < 0.05), and remained elevated during 3 h of post-exercise recovery in both sexes (P < 0.05), but with a greater relative increase in men than women (P < 0.05). Plasma FA oxidation (Rox) increased during exercise with no difference between intensities, and it remained elevated during 3 h of post-exercise recovery in both sexes (P < 0.05). Total lipid oxidation (Lox) was elevated in both sexes, but more in men during 3 h of post-exercise recovery on D1 (P < 0.05) and remained elevated on D2 in men, but not in women (P < 0.05). There were no differences between E45 and E65 for post-exercise energy substrate turnover or oxidation in men and women as energy expenditure of exercise (EEE) was matched between bouts. We conclude that the impact of exercise upon lipid metabolism persists into recovery, but that women depend more on lipid during exercise whereas, during recovery, lipid metabolism is accentuated to a greater extent in men.