Women of reproductive age need reliable and effective family planning methods to manage their fertility. Natural family planning (NFP) methods or fertility awareness-based methods (FABMs) have been increasingly used by women due to their health benefits. Nevertheless, effectiveness of these natural methods remains inconsistent, and these methods are difficult for healthcare providers to implement in their clinical practice. The purpose of this study is to evaluate the effectiveness of the Marquette Model NFP system to avoid pregnancy for women at multiple teaching sites using twelve months of retrospectively collected teaching data. Survival analysis (Kaplan–Meier) was used to determine typical unintended pregnancy rates for a total of 1,221 women. There were forty-two unintended pregnancies which provided a typical use unintended pregnancy rate of 6.7 per 100 women over twelve months of use. Eleven of the forty-two unintended pregnancies were associated with correct use of the method. The total unintended pregnancy rate over twelve months of use was 2.8 per 100 for women with regular cycles, 8.0 per 100 women for the postpartum and breastfeeding women, and 4.3 per 100 for women with irregular menstrual cycles. The Marquette Model system of NFP was effective when provided by health professionals who completed the Marquette Model NFP teacher training program.