The issue of insufficient physical activity among computer game players remains relevant. This study proposes a solution based on the comprehensive use of gaming-oriented mobile applications for the conditioning training of esports athletes. A sequential pedagogical experiment was conducted to determine the effectiveness of esports athletes applying an aerobic-focused conditioning training program (slow running). The program’s unique feature is its implementation in a remote format using mobile applications for planning, execution, control, and performance evaluation. It is based on an original concept of implementing running training in the form of a mobile running application (the so-called “exergame”) with a game-like nature (“Zombies, Run!”). The program was designed for a six-week implementation. Its effectiveness was determined by evaluating the dynamics of indicators: 1600 m run time; calculated maximal oxygen consumption (VO2 max); and heart rate (HR). Subjective attitudes towards the program’s physical loads were assessed using the Rating of Perceived Exertion (RPE) scale and the Physical Activity Satisfaction Needs scale. It was found that esports athletes significantly (p<0.05) improved their 1600 m run time, VO2 max, and HR indicators under the influence of the slow running program. Along with the volume and intensity increase of the running load, a decrease in RPE scale indicators was observed. The obtained data confirmed the advantages of the comprehensive use of mobile applications for normalizing the motor activity of esports athletes in the form of conditioning training. Both the remote format of planning and accounting and the game format of activities contributed to increasing the engagement of esports athletes in physical activity. The effectiveness of the slow running training program for esports athletes using mobile applications was established in terms of increasing physical activity (regular, organized physical activity), improving physical fitness (duration and volume of slow running), enhancing physical condition (VO2 max, HR), and interest in physical activity (adherence).