Subjective tinnitus is the perception of a sound without any external source. Repetitive transcranial magnetic stimulation (rTMS) has been examined as a treatment tool for chronic tinnitus for several years trying to target hyperactivity/abnormal synchronization within the auditory cortex putatively underlying the auditory phantom percept. However, its exact impact on auditory cortical activity remains largely unknown. This study's objective was to systematically examine changes in auditory responses (N1, auditory steady-state response [aSSR]) measured by means of magnetoencephalography after single sessions of stimulation with different TMS paradigms. Subjects with chronic tinnitus (n = 10) underwent five sessions of rTMS in which they received one of five different stimulation protocols (1 Hz, individual alpha frequency, continuous theta burst stimulation [cTBS], intermittent theta burst stimulation [iTBS], and sham) in randomized order using a single-blind study design. Cortical steady-state responses to 40 Hz amplitude-modulated tones were measured before and after each magnetic stimulation protocol. The results demonstrate a reduction of the cortical response to the auditory steady-state stimulus after magnetic stimulation, whereas the N1 response was slightly enhanced or remained unchanged. Furthermore, reduction of the aSSR was driven by effects of iTBS, cTBS, and 1 Hz stimulation. Correspondingly, behavioral measures demonstrated the greatest reduction of tinnitus loudness after the respective rTMS protocols. The current study offers an interesting insight into the effects of rTMS on auditory cortical activity. The results of the study are discussed in the context of current limitations of TMS for the treatment of chronic tinnitus.