Prolonged sperm storage over winter is a common feature of reproduction in some bats. In order to understand how sperm storage in the female genital tract of the vespertilionid bat, Scotophilus heathi (Greater yellow bat), is controlled, we compared concentrations of glucose and the fatty-acid carrier carnitine in the blood, and carnitine concentrations and levels of expression of the glucose transporters (GLUTs) and the carnitine transporter OCTN2 in the utero-tubal junction of females during non-storage (early winter) and sperm-storage periods (late winter-early spring). During the sperm-storage period (December–January) blood glucose concentrations declined, as did the expression of GLUT3 and GLUT5 in the utero-tubal junction. At the same time there were increases in the concentration of carnitine, and expression of OCTN2 and hormone-sensitive lipase (HSL) in the utero-tubal junction. These results suggest that prolonged sperm storage is enhanced by decreased glucose availability but increased free fatty acid availability at the site of sperm storage. Increases in expression of GLUT4 and GLUT8 in late winter suggest a role for these GLUTs in increasing sperm motility prior to fertilization. J. Exp. Zool. 319A: 517–526, 2013. © 2013 Wiley Periodicals, Inc.