Estradiol (E2) has been implicated in sexual functioning in both sexes. E2 levels change distinctively over the menstrual cycle, peaking around ovulation. Data on short-term effects of fluctuating E2 levels on sexual desire are however sparse and mostly based on observational studies. To fill this gap, we ran a double-blind, randomized, placebo-controlled study (N = 126) to investigate the effects of a short-term increase in E2 on sexual desire and orgasm frequency in healthy, young men and women. Circulating E2 levels were elevated through estradiol valerate (E2V) administered over two consecutive days to simulate the rise in E2 levels around ovulation. E2V had no effect on orgasm frequency and only minor effects on sexual desire. On average, the administered E2V dampened change in sexual desire compared to untreated participants with comparable baseline sexual desire in such a way that sexual desire was slightly reduced even in those with higher baseline sexual desire. These findings suggest that short-term increases in E2 have little effect on sexual function and are unlikely to explain the increase in sexual desire around ovulation.