Research on action-based timing has shed light on the temporal dynamics of sensorimotor coordination. This study investigates the neural mechanisms underlying action-based timing, particularly during finger-tapping tasks involving synchronized and syncopated patterns. Twelve healthy participants completed a continuation task, alternating between tapping in time with an auditory metronome (pacing) and continuing without it (continuation). Electroencephalography data were collected to explore how neural activity changes across these coordination modes and phases. We applied deep learning methods to classify single-trial electroencephalography data and predict behavioral timing conditions. Results showed significant classification accuracy for distinguishing between pacing and continuation phases, particularly during the presence of auditory cues, emphasizing the role of auditory input in motor timing. However, when auditory components were removed from the electroencephalography data, the differentiation between phases became inconclusive. Mean accuracy asynchrony, a measure of timing error, emerged as a superior predictor of performance variability compared to inter-response interval. These findings highlight the importance of auditory cues in modulating motor timing behaviors and present the challenges of isolating motor activation in the absence of auditory stimuli. Our study offers new insights into the neural dynamics of motor timing and demonstrates the utility of deep learning in analyzing single-trial electroencephalography data.