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Visual Abstract, Binaural beating is a perceptual auditory illusion occurring when presenting two neighboring frequencies to each ear separately. Several controversial claims have been attributed to binaural beats regarding their ability to entrain human brain activity and mood, in both the scientific literature and the marketing realm. Here, we sought to address those questions in a robust fashion using a single-blind, active-controlled protocol. To do so, we compared the effects of binaural beats with a control beat stimulation (monaural beats, known to entrain brain activity but not mood) across four distinct levels in the human auditory pathway: subcortical and cortical entrainment, scalp-level functional connectivity and self-reports. Both stimuli elicited standard subcortical responses at the pure tone frequencies of the stimulus [i.e., frequency following response (FFR)], and entrained the cortex at the beat frequency [i.e., auditory steady state response (ASSR)]. Furthermore, functional connectivity patterns were modulated differentially by both kinds of stimuli, with binaural beats being the only one eliciting cross-frequency activity. Despite this, we did not find any mood modulation related to our experimental manipulation. Our results provide evidence that binaural beats elicit cross frequency connectivity patterns, but weakly entrain the cortex when compared with monaural beat stimuli. Whether binaural beats have an impact on cognitive performance or other mood measurements remains to be seen and can be further investigated within the proposed methodological framework.