This study describes the weekly variations of well-being ratings relative to fatigue (wFatigue), stress (wStress), delayed-onset muscle soreness (wDOMS), sleep quality (wSleep), and Hooper questionnaire (wHQ) throughout the season. In addition, the well-being variables for the playing position in different moments of the season were discussed. Twenty-one elite young soccer players U17 took part in this study. From the beginning of the pre-season, well-being status was monitored daily by the HQ method throughout 36 weeks, including four periods: (1) pre-season, (2) early-season, (3) mid-season, and (4) end-season. Players trained at least 3 times per week throughout the season. The main outcome was that, in weeks 33 and 28, the highest [wFatigue: 15.85 ± 3.38 arbitrary units (AU); wHQ: 48.86 ± 9.23 AU] and the lowest (wFatigue: 5.38 ± 1.88 AU; wHQ: 20.43 ± 5.49 AU) wFatigue and wHQ occurred, respectively, although the lowest level of wDOMS happened in week 28 (4.86 ± 2.15 AU), while the highest wDOMS was observed in week 5 (14.65 ± 4.16 AU). The highest wSleep (13.00 ± 2.12 AU) and wStress (11.65 ± 2.92 AU) were observed in weeks 8 and 34, respectively, while the lowest wSleep (5.81 ± 2.29 AU) and wStress (3.76 ± 0.94 AU) were marked in week 29 coincidentally. In the HQ between every weekday, except recovery day, and the day of the match (MD), considerable highest HQ was only revealed in 2 days after MD in contrast to overall team comparison. In the present study, we observed that the well-being changes between different phases of the season as well as between weeks and days of the week with the MD are significant. These results provide a great point of view for coaches and practitioners about well-being variations over a season in elite youth soccer level. As a result, coaches will be more aware about non-functional overreaching and taking measures to prevent it.