Scrapie, a production limiting disease of sheep and goats, is part of a family of diseases known as transmissible spongiform encephalopathies (TSEs). Canada conducts active and passive scrapie surveillance of the national goat herd and sheep flock with the goal of achieving eradication of scrapie and of meeting World Organisation for Animal Health (OIE) requirements for freedom from disease. Risk-based disease surveillance is commonly used for surveillance of non-highly contagious animal diseases because it is more resource efficient than traditional random sampling methods. It was found that the surveillance system’s sensitivity trended upwards from 2013 to 2016. It was also found that risk-based sampling can be used to reduce required minimum sample sizes. Furthermore, by implementing a risk-based surveillance system, the sample size required to meet surveillance targets will decrease over time with the decrease in scrapie prevalence as a result of the success of scrapie eradication efforts in Canada. Canada’s scrapie surveillance efforts are sufficient but can be made more efficient by implementing risk-based surveillance.