Repetitive Transcranial Magnetic Stimulation (rTMS) provides a unique opportunity to study causal relationships between activity in the dorsolateral prefrontal cortex (DLPFC) and executive functioning, by modulating brain activity in SHAM controlled designs. We devised a new Stroop task paradigm in which subjects must engage in both strategic and automatic attentional processes. In the current experiment, we manipulated subjects' expectancies for incongruent stimuli. Previous research demonstrated that when subjects have a high level of expectancy that a stimulus will be incongruent, they are able to strategically adjust the relative influence of word reading on color naming. The effect of high frequency (HF) rTMS on Stroop performance of 20 right-handed healthy female volunteers was tested using a double blind within subjects design by counterbalanced crossover sham (placebo) and active rTMS over the right DLPFC. Since mood remained unchanged after rTMS, the Stroop data could be evaluated independent of mood changes. Only in the high expectancy condition, we found a decreased response time to both congruent and incongruent trials on the Stroop task performance after HF rTMS. The SHAM placebo condition yielded no effects. We conclude that high frequency stimulation over the right DLPFC has an effect on top-down attentional processes by modulating the attentional set.