Slow paced breathing has been demonstrated to provide significant health benefits for a person’s health, and, during breathing sessions, it is desirable to monitor that a person is actually compliant with the breath pacer. We explore the potential use of pulse rate variability to monitor compliance with a breath pacer during meditation sessions. The study involved 6 human subjects each participating in 2–3 trials, where they are asked to follow or not to follow the breath pacer, where we collected data on how the magnitude of pulse rate variability changed. Two methods, logistic regression and a running standard deviation technique, were developed to detect non-compliance with the breath pacer based on pulse rate variability metrics. Results indicate that using pulse rate variability alone may not reliably detect non-compliance with the breath pacer. Both models exhibited limitations in terms of false positives and false negatives, with accuracy ranging from 67 to 65%. Existing methods involving visual, audio, and motion signals currently perform better for monitoring compliance with the breath pacer.