This study analyzed weekly training and match loads through respiratory and muscular ratings of perceived exertion (RPEres and RPEmus) and investigated the relationship between differential RPE-training loads (TL) and fitness changes in rugby union players. Twenty-eight males from the U16 and U18 teams of the same club completed a 10-week longitudinal observational study with testing sessions (i.e., a countermovement jump, a 10-m running sprint and a 1.2-km shuttle run) before and after the monitoring phase. No changes in physical fitness were observed after this period (p > 0.05). RPEres-TL and RPEmus-TL four days before the match-day (MD−4) were greater than on the MD−2 (RPEres-TL: p = 0.004, d = 0.73; RPEmus-TL: p = 0.001, d = 1.02) and on the MD (RPEres-TL: p < 0.001, d = 0.90; RPEmus-TL: p < 0.001, d = 1.16) in U16 players. In U18 players, RPEmus-TL was higher on the MD−4 than on the MD−2 (p = 0.045, d = 0.73), while the dRM-Index (respiratory/muscular ratio) was higher on the MD−2 than on the MD−4 (p = 0.042, d = 0.55). No significant differences were found between RPEres-TL and RPEmus-TL for any session (p > 0.05). The accumulated RPEres-TL (p = 0.018, r = 0.59) and RPEmus-TL (p = 0.001, r = 0.76) were positively correlated with changes in shuttle running test performance in U18 players. Differential RPE-TLs provide additional insights to analyze and differentiate weekly load distribution between categories, and partially indicates fitness changes: players who accumulated more perceived loads during the season tended to maintain endurance performance. This practical available monitoring approach can assist academy rugby union practitioners in further individualizing training and optimizing performance.