Children with developmental coordination disorder (DCD) display difficulties in perception-action coupling when engaging in tasks requiring predictive timing. We investigated the influence of awareness on auditory-motor adjustments to small and large rhythmic perturbations in the auditory sequence to examine whether children synchronize their movements automatically or through planning and whether those adjustments occur consciously or subconsciously. Electroencephalography (EEG) was used to assess functional connectivity patterns underlying different adjustment strategies. Thirty-two children aged 7–11 participated, including children with DCD and their typically developing (TD) peers with and without musical training. All children automatically adjusted their motor responses to small rhythmic perturbations by employing the anticipatory mode, even when those changes were consciously undetectable. Planned adjustments occurred only when children consciously detected large fluctuations (Δ 20%), which required a shift from predictive to reactive strategies. Compared to TD peers, children with DCD showed reduced interhemispheric connectivity during planned adjustments and displayed similar neural patterns regardless of task constraints. Notably, they benefited from rhythmic entrainment despite having increased variability and lower perceptual acuity. Musical training was associated with enhanced auditory-perceptual timing, reduced variability, and increased interhemispheric coherence. These insights are important for the therapeutic application of auditory/rhythm-based interventions in children with DCD.