Simulation models were developed to quantify the likelihood of equine influenza virus infection entering pre‐movement isolation, persisting through pre‐ and post‐movement isolation periods without being detected by scheduled laboratory testing, and escaping to infect susceptible horses at a destination. The mean probability of escape ranged from 1 in 1,200,000 to 1 in 600,000 depending on lot size. For 95% of iterations the probability of escape was less than 1 in 200,000, regardless of lot size. For a large group of 600 horses processed as multiple separate lots, the mean probability of escape ranged from 1 in 10,000 to 1 in 56,000 depending on lot size. As a result of this analysis, a modified protocol, with two tests during pre‐movement isolation and an additional test during post‐movement isolation at the Chief Veterinary Officer's discretion, was implemented.