The purpose of this study is to considerate the prediction formula for marathon time based on 20-m shuttle run test and training indexes in recreational runners. 100 male and 111 female recreational runners who have experienced one or more marathon races were measured. Each participant was measured with regard to physical characteristics, 20-m shuttle run test, and answered questionnaires about his/her training (monthly running distance, frequency of training, and years of experience of running training). Moreover, participants self-reported their best marathon time. Additionally, to examine the validity of the prediction formula, 14 male and 13 female recreational runners were measured using the 20-m shuttle run test and they answered the questionnaires about his/her training. The marathon time was significantly correlated with the participant’s BMI, the times of 20-m shuttle run test, the monthly running distance, the frequency of training and the years of experience of running training for both male and female runners. Subsequently, multiple regression analysis generated the prediction model for marathon time by the measurement items. Furthermore, in the examination of the validity of the prediction formula, predicted marathon time was significantly highly correlated with measured marathon time. This study suggested that the marathon time can be predicted by the 20-m shuttle run test, the monthly running distance, and the years of experience of running training and the predicted marathon time may be useful for the marathon race and training in recreational runners.