Differences in core temperature and body heat content, generally observed between the luteal and follicular phase of the menstrual cycle, have been reported to modulate the thermogenic activity of cold-exposed women. However, it is unclear how this change in whole body shivering activity will influence fuel selection. The goal of this study was to quantify the effects of the menstrual cycle on muscle recruitment and oxidative fuel selection during low-intensity shivering. Electromyographic activity of eight large muscles was monitored while carbohydrate, lipid, and protein utilization was simultaneously quantified in the follicular and luteal phases of the menstrual cycle in nonacclimatized women shivering at a low intensity. The onset (∼25 min), intensity (∼15% of maximal voluntary contraction), and pattern (∼6 shivering bursts/min) of the shivering response did not differ between menstrual cycle phases, regardless of differences in core temperature and hormone levels. This resulted in lipids remaining the predominant substrate, contributing 75% of total heat production, independent of menstrual phase. We conclude that hormone fluctuations inherent in the menstrual cycle do not affect mechanisms of substrate utilization in the cold. Whether the large contribution of lipids to total heat production in fuel selection confers a survival advantage remains to be established.