The aim of this study was to examine the effect of a 12-week intervention program on motivational climate in physical education (PE) lessons, on female adolescents' self-efficacy for independent training in leisure time, and on physical fitness measures. Participants were 154 female high school students divided into three groups: (1) received a program to enhance motivation for physical activity (PA) during PE lessons and in leisure time, using the internet; (2) followed the regular curriculum in addition to self-report at the end of each lesson, using smartphone application; (3) engaged in standard PE lesson activities. A self-efficacy for training questionnaire, a motivational climate questionnaire, and tests of physical fitness were administered. Findings indicated improvement pre-post in motivational climate and in the physical fitness measures, and a decline in the intensity of negative affect towards running, in all three groups. Incorporating innovative ways, and promoting self-accountability using self-documentation encourage students to exercise during their leisure time.