Throughout the 1990s the expense and lack of availability of eflornithine limited its use. However, in the early 2000s demand for eflornithine significantly increased because it was found to be more effective than melarsoprol in the treatment of late-stage Gambian sleeping sickness. Eflornithine inhibits an enzyme called ornithine decarboxylase, which catalyzes the synthesis of amine-based compounds involved in cell division and cell differentiation. In order to circumvent the evolution of eflornithine-resistant trypanosomes, combination therapies are being developed. The most effective of these is the combination of eflornithine with nifurtimox, a nitrofuran compound that is used in the treatment of Chagas disease (Chagas' disease), which is caused by T. cruzi, an organism closely related to T. brucei.

Because eflornithine was shown to block the proliferation of tumour cells, its use in the treatment of certain cancers (cancer) has been investigated. However, the results of such studies have been mixed. The most promising anticancer use of eflornithine is as a topical chemopreventative agent for people at high risk of skin cancer.