In the present study we tested the hypothesis that, in subjects with Asperger’s syndrome (ASP), the dynamics of language‐related regions might be abnormal, so that repetitive transcranial magnetic stimulation (rTMS) over Broca’s area leads to differential behavioral effects as seen in neurotypical controls. We conducted a five‐stimulation‐site, double‐blind, multiple crossover, pseudo‐randomized, sham‐controlled study in 10 individuals with ASP and 10 age‐ and gender‐matched healthy subjects. Object naming was assessed before and after low‐frequency rTMS of the left pars opercularis, left pars triangularis, right pars opercularis and right pars triangularis, and sham stimulation, as guided stereotaxically by each individual’s brain magnetic resonance imaging. In ASP participants, naming improved after rTMS of the left pars triangularis as compared with sham stimulation, whereas rTMS of the adjacent left opercularis lengthened naming latency. In healthy subjects, stimulation of parts of Broca’s area did not lead to significant changes in naming skills, consistent with published data. Overall, these findings support our hypothesis of abnormal language neural network dynamics in individuals with ASP. From a methodological point of view, this work illustrates the use of rTMS to study the dynamics of brain–behavior relations by revealing the differential behavioral impact of non‐invasive brain stimulation in a neuropsychiatric disorder.