This disclosure relates to transdermal pharmaceutical compositions containing progesterone in combination with one or more solubilizing agents and penetration enhancers, wherein the pharmaceutical compositions are formulated as creams for topical administration. In some embodiments, the transdermal pharmaceutical compositions contain progesterone, a medium-chain oil, and d-limonene. In some embodiments, the transdermal pharmaceutical compositions contain progesterone, a medium-chain oil, a penetration enhancer (e.g., propylene glycol, a fatty acid ester of propylene glycol, a glycol ether), and optionally d-limonene. In certain embodiments, the pharmaceutical compositions further include estradiol. Methods for treating conditions associated with hormone deficiency in a subject are also described.