Exercise and physical activity have proven benefits for physical and psychological well-being. However, it is not clear if healthy young adults can enhance mood in everyday life through regular exercise. Earlier studies mainly showed positive effects of acute exercise and exercise programs on psychological well-being in children, older people and in clinical populations. Few studies controlled participants' physical activity in daily life, performed besides the exercise program, which can impact results. In addition the transition from mood enhancement induced by acute exercise to medium or long-term effects due to regular exercise is not yet determined. The purpose of this pilot study was to examine the acute effects of an aerobic running training on mood and trends in medium term changes of mood in everyday life of young adults. We conducted a 10-week aerobic endurance training with frequent mood assessments and continuous activity monitoring. 23 apprentices, separated into experimental and control group, were monitored over 12 weeks. To control the effectiveness of the aerobic exercise program, participants completed a progressive treadmill test pre and post the intervention period. The three basic mood dimensions energetic arousal, valence and calmness were assessed via electronic diaries. Participants had to rate their mood state frequently on 3 days a week at five times of measurement within 12 weeks. Participants' physical activity was assessed with accelerometers. All mood dimensions increased immediately after acute endurance exercise but results were not significant. The highest acute mood change could be observed in valence (p = 0.07; η(2) = 0.27). However, no medium term effects in mood states could be observed after a few weeks of endurance training. Future studies should focus on the interaction between acute and medium term effects of exercise training on mood. The decreasing compliance over the course of the study requires the development of strategies to maintain compliance over longer periods