The purpose of this study was to examine the usefulness of the rating of perceived exertion training load for monitoring changes in several aerobic fitness and neuromuscular performance variables during 9 weeks of soccer training in young professional players. Nineteen male soccer players (20.2 ± 1.9 years) belonging to the same reserve team of a Spanish La Liga Club participated in this study. Countermovement jump (CMJ), CMJ arm swing, single leg CMJ, a sprint running test (i.e., 5 m and 15 m times) and an aerobic fitness running test were performed at the start of the pre-season (Test 1) and 9 weeks later (Test 2). During 9 weeks, after each training session and match, players reported their rating of perceived exertion (RPE) separately for respiratory (RPEres) and leg musculature (RPEmus) effort. The training load (TL) was calculated by multiplying the RPE value by the duration in minutes of each training session or match. Accumulated RPEmus, and associated TL, as well as accumulated training volume were negatively correlated with the changes in most physical fitness attributes after 9 weeks of training (r = -0.51 to -0.64). Present results suggest that a high perception of leg muscular effort associated with training sessions and matches, as well as an excessive accumulation of training volume (time), can impair the improvement in several physical fitness variables believed to be relevant for on-field soccer performance. Therefore, the independent assessment of leg muscular effort to quantify TL can be an interesting additional monitoring measure in soccer training.