Introduction To investigate the risk factors for myopia progression in primary school children and build prediction models by applying machine learning to longitudinal, cycloplegic autorefraction data. Methods A total of 2740 children from grade 1 to grade 6 were examined annually over a period of 5 years. Myopia progression was determined as change in cycloplegic autorefraction. Questionnaires were administered to gauge environmental factors. Each year, risk factors were evaluated and prediction models were built in a training group and then tested in an independent hold-out group using the random forest algorithm. Results Six variables appeared in prediction models on myopia progression for all 5 years, with combined weight of 77% and prediction accuracy over 80%. Uncorrected distance visual acuity (UDVA) had the greatest weight (mean 28%, range 22-39%), followed by spherical equivalent (20%, 7-28%), axial length (13%, 10-14%), flat keratometry reading (K1) (7%, 4-11%), gender (6%, 2-9%), and parental myopia (3%, 1-10%). UDVA and spherical equivalent had peak weight at the second and third study years, respectively. The weight of myopic parents decreased steadily over the 5 years (9.5%, 1.9%, 1.8%, 1%, and 1.3%). Weekly time spent reading, reading distance, reading in bed, and frequency of eating meat were included as variables in different study years. Conclusions Myopia progression in children was predicted well by machine learning models. UDVA and spherical equivalents were good predictive factors for myopia progression in children through primary school. Parental myopia was found to play a substantial role in the early stage of myopia progression but waned as children grew older.