The aim of this study was two-fold: (i) analyze the weekly variations of well-being and training/match intensity measures in youth soccer players, and (ii) test relations between well-being and training intensity outcomes. The study followed a descriptive case study design. Twenty-seven under-17 male soccer players were monitored for well-being and training intensity parameters over seventeen consecutive weeks. An adjusted version of the Hooper questionnaire was used to monitor the perceptive sleep quality, readiness, fatigue, and delayed onset muscle soreness (DOMS) early in the morning. The CR-10 Borg’s scale was also used for monitoring the rate of perceived exertion (RPE) of players after training sessions. Repeated-measures analysis of variance was executed to test the between-week variations of both well-being and training intensity outcomes. Moreover, Pearson product moment correlation was used to test the relations between well-being and training intensity outcomes. Repeated measures ANOVA revealed significant differences between weeks in the sleep quality (F = 0.422; p < 0.001; ηp2 = 0.140), readiness (F = 0.8.734; p < 0.001; ηp2 = 0.251), fatigue (F = 4.484; p < 0.001; ηp2 = 0.147), DOMS (F = 3.775; p = 0.001; ηp2 = 0.127), RPE (F = 7.301; p < 0.001; ηp2 = 0.219), and session-RPE (F = 17.708; p < 0.001; ηp2 = 0.405). Correlations between well-being and training intensity outcomes in the same week revealed moderate correlations between fatigue and session-RPE (r = 0.325). As conclusions, it was found that well-being and training intensity fluctuates over the season, while well-being outcomes seems to be related with training intensity, although with a small magnitude.