The purpose of this study was to conduct a systematic review of the pharmacological options available to treat patients diagnosed with attention-deficit hyperactivity disorder and anxiety disorder, for generating evidence on the safest, most-effective and tolerable pharmacotherapy. To this end, a systematic search was performed in three electronic databases (Medline, Scopus and Directory of Open Access Journals; December 2017). Randomized, double-blind, parallel-design clinical trials evaluating the efficacy, safety or tolerability of therapies for attention-deficit hyperactivity disorder and anxiety disorder in children and adolescents or adults were considered. A total of 1960 articles were retrieved from the databases, of which five studies were included in the qualitative synthesis. Two of these studies evaluated the drug atomoxetine, another study evaluated desipramine, and the remaining two studies evaluated methylphenidate, with fluvoxamine being associated with methylphenidate in one of the trials. Owing to the high heterogeneity among studies, it was not possible to combine data for meta-analyses. Although only few studies have been evaluated in this systematic review, the results point to a more significant benefit of atomoxetine. This is probably because this drug was studied in a wider age range and evaluated by more specific scales for both disorders. To further strengthen this evidence, randomized, controlled and multicenter clinical trials with larger sample sizes should be conducted.