Background: Sexual disorders are the most common clinical manifestations of hypogonadism. Functional hypogonadism is the most frequent form, and clomiphene citrate (CC) has been recently introduced as a possible off-label therapeutic option for these patients. Objective: This study aimed to evaluate the effects of CC on the overall sexual function in dysmetabolic obese men with low testosterone (T) levels. Methods: This was a sub-study of a randomized, double-blind, cross-over, placebo-controlled trial that included twenty-four obese or overweight subjects with impaired glucose tolerance or type 2 diabetes and confirmed low total T (≤10.4 nmol/l) levels. Subjects were treated with CC or placebo (Plac) for 12 weeks, with an interval wash-out period of 6 weeks between treatments. All subjects were on metformin 2gr/day and a low-calorie diet. The between-treatment difference in the overall sexual function was assessed by IIEF-15 and a qADAM questionnaire. Results: IIEF-15 and qADAM questionnaire data were available for 18 individuals. In unadjusted analyses, CC was associated with lower IIEF-15 total, erectile function, and intercourse satisfaction domain scores than Plac. After adjustments for multiple variables, CC was associated with a higher IIEF-15 sexual desire domain score (+0.9 ± 0.8; p<.001) despite a lower qADAM score (-2.1 ± 0.9; p=.008) with respect to Plac. No differences were found for the other domains between groups. Discussion: The clinical significance of the absolute changes in IIEF-15 and qADAM scores during CC versus Plac is limited. However, CC has a reliable effect on sexual desire and is also as safe as Plac. According to the sample size, duration of follow-up, and inclusion criteria defined for the main study, further studies are therefore needed to assess the long-term efficacy of CC. Conclusion: Compared to Plac, CC was found to be associated with a neutral effect on overall sexual function.