No previous study has analyzed the differences in the effectiveness of an intervention with mobile applications, according to gender and academic year, on the level of physical activity, body composition, and physical fitness of adolescents. For this reason, the aim of the present investigation was to establish the differences in the change in level of physical activity, kinanthropometric and derived variables, and fitness with an intervention to promote physical activity base on the use of mobile applications in adolescents according to gender and academic year. A randomized controlled trial was carried out with a 10-week intervention with mobile applications that was promoted by the physical education department of the school. The final sample consisted of 400 adolescents (210 males and 190 females; mean age: 13.96 ± 1.21 years). A total of 240 adolescents were placed in the experimental group, and 160 were placed in the control group. Physical activity, body composition and physical fitness were measured before (pre) and after the intervention (post). During the intervention, four apps were mandatory used by the adolescents (Strava, Pacer, MapMyWalk, Pokémon Go) a minimum of three times a week. The distance to be traveled increased weekly during the intervention. The control group did not use the apps but continued to perform their physical activities as normal. The results showed that the use of mobile apps was higher in females (p < 0.001; 71.1% females vs 50.0% males) and adolescents in higher academic year (p < 0.001; 74.4% fourth academic year vs 53.8% first academic year). Moreover, the use of the apps prevented the increase of variables related to fat accumulation (body mass index (BMI), fat mass, sum 3 skinfolds, waist, and hips girths). Specifically, the differences between male and female were significant in BMI (p < 0.001; mean diff: −0.352), corrected calf girth (p = 0.008; mean diff: −0.498), fat mass (p = 0.025; mean diff: 0.748), handgrip right (p = 0.002; mean diff: −1.359), handgrip left (p = 0.002; mean diff: −1.103), and countermovement jump (p = 0.002; mean diff: −2.456), while when considering academic year, differences were significant in height (p < 0.001–0.044; mean diff: −1.099 to −0.509), sum of 3 skinfolds (p = 0.046–0.047; mean diff: −3.255), waist girth (p = 0.048; mean diff: 0.584), hip girth (p < 0.001–0.008; mean diff: −1.461 to −0.777), corrected calf girth (p = 0.019–0.029; mean diff: −0.539 to −0.482), and fat mass (p = 0.025–0.046; mean diff: 1.011 to −1.392). It can be concluded that mobile apps can be a great alternative to promote the practice of physical activity, decrease of fat variables, and improve some physical fitness variables, especially in females and adolescents in higher academic year. As a consequence of the above, gender and academic year should be considered in future interventions with mobile apps, as the effects in kinanthropometric and derived variables, and fitness and the follow-up of the intervention by adolescents may be different depending on these factors. The research protocol was registered prior to the start of the study in ClinicalTrials.gov (code: NCT04860128), under the name “New technologies as a tool for health promotion in schoolchildren of compulsory secondary education”. https://clinicaltrials.gov/ct2/show/NCT04860128?term=NCT04860128&draw=2&rank=1.