Enclomiphene is primarily used as a treatment for men with persistent low testosterone as a result of secondary pogonadotropic pogonadism. In secondary pogonadotropic pogonadism, the resulting low levels of testosterone is attributed to inadequacies in the pothalamic-pituitary-gonadal axis. In contrast, primary pogonadism is caused by defects in the testes that causes them to be unable to produce the required amount of testosterone.

Enclomiphene, which stimulates the endogenous production of testosterone, is not currently known to have common adverse effects of exogenous testosterone replacement therapy, such as reduced spermatogenesis or infertility.