Speed is an essential parameter in biomechanical analysis and general locomotion research. It is possible to estimate the speed using global positioning systems (GPS) or inertial measurement units (IMUs). However, GPS requires a consistent signal connection to satellites, and errors accumulate during IMU signals integration. In an attempt to overcome these issues, we have investigated the possibility of estimating the horse speed by developing machine learning (ML) models using the signals from seven body-mounted IMUs. Since motion patterns extracted from IMU signals are different between breeds and gaits, we trained the models based on data from 40 Icelandic and Franches-Montagnes horses during walk, trot, tölt, pace, and canter. In addition, we studied the estimation accuracy between IMU locations on the body (sacrum, withers, head, and limbs). The models were evaluated per gait and were compared between ML algorithms and IMU location. The model yielded the highest estimation accuracy of speed (RMSE = 0.25 m/s) within equine and most of human speed estimation literature. In conclusion, highly accurate horse speed estimation models, independent of IMU(s) location on-body and gait, were developed using ML.