The research focuses on learning methods that address individual differences, motivation and training goals in fitness running. The aim was to examine the possibilities of use of fitness trackers in smart phones for fitness running lessons. The core of the study was to design and implement an innovative blended learning model to individualize the training process, personalize the lessons, and thus enhance students' motivation to participate. Fitness tracking applications provided quantified information about the training process via an online data analysis platform. The model was implemented and evaluated in a three-year survey. 278 students enrolled fitness running in the followed periods. Evaluation concerned fitness tracker applicability, analysis of students' motivation to run, and development of attendance between the experimental and control periods. Major performance characteristics were described in the selected runners to get further information about the training process. Fitness tracking combined with teacher's coaching and peer-evaluation support seems to be an efficient means to enhance students' motivation and increase the attendance. The enrolment increased three times and the drop-out rate decreased by 16%. The highest rated educational benefit of the new learning model was found in inclusion of regular physical activity in students' weekly schedule.