Background The effect of various drugs was investigated by using transcranial magnetic stimulation (TMS) both in healthy subjects and patients, and the results indicated an influence of antidepressant drugs (ADs) on motor excitability. Objective The aim of our study was to analyze the effects of two ADs, the tricyclic (TCA) clomipramine and the serotoninergic antidepressant (SSRI) citalopram on the motor cortex excitability in major depressed patients with TMS. Methods Thirty affected subjects were placed into three groups: two received an intravenous dose of 25 mg clomipramine or 40 mg citalopram, and one received an injection of a placebo. Motor cortex excitability was studied by single and paired TMS before and after 3.5, 8, and 24 hours from administration of the drugs and placebo. Motor cortical excitability was measured using different TMS parameters: resting motor threshold (RMT), motor-evoked potential (MEP) amplitude, intracortical inhibition (ICI), and intracortical facilitation (ICF). Results The results indicated a temporary but significant increase of RMT and ICI and a decrease of ICF after the administration of both drugs, with a longer inhibition for the clomipramine rather than the citalopram. MEP amplitude was not significantly affected by the antidepressant injections. Conclusions Our findings highlight that a single intravenous dose of clomipramine or citalopram exerts a significant but transitory suppression of motor cortex excitability in depressed patients. TMS represents a useful research tool in assessing the effects of motor cortical excitability of drugs used in the treatment of mental disorders.