Cluster sets (CS) are effective in maintaining performance and reducing perceived effort compared to traditional sets (TRD). However, little is known about these effects on adolescent athletes. The purpose of this study was to compare the effect of CS on the performance of mechanical and perceptual variables in young athletes. Eleven subjects [4 boys (age = 15.5 ± 0.8 years; body mass = 54.3 ± 7.0 kg; body height = 1.67 ± 0.04 m; Back Squat 1RM/body mass: 1.62 ± 0.19 kg; years from peak height velocity [PHV]: 0.94 ± 0.50) and 7 girls (age = 17.2 ± 1.4 years; body mass = 54.7 ± 6.3 kg; body height = 1.63 ± 0.08 m; Back Squat 1RM/body mass: 1.22 ± 0.16 kg; years from PHV: 3.33 ± 1.00)] participated in a randomized crossover design with one traditional (TRD: 3 × 8, no intra-set and 225 s interest rest) and two clusters (CS1: 3 × 2 × 4, one 30 s intra-set and 180 s inter-set rest; and CS2: 3 × 4 × 2, three 30 s intra-set and 90 s inter-set rest) protocols. The subjects were assessed for a Back Squat 1RM for the first meet, then performed the three protocols on three different days, with at least 48 h between them. During experimental sessions, a back squat exercise was performed, and mean propulsive velocity (MPV), power (MPP), and force (MPF) were collected to analyze performance between protocols, together with measures of countermovement jump (CMJ) and perceptual responses through Rating of Perceived Exertion for each set (RPE-Set) and the overall session (S-RPE), and Muscle Soreness (DOMS). The results showed that velocity and power decline (MVD and MPD) were favorable for CS2 (MVD: -5.61 ± 14.84%; MPD: -5.63 ± 14.91%) against TRD (MVD: -21.10 ± 11.88%; MPD: -20.98 ± 11.85%) (p < 0.01) and CS1 (MVD: -21.44 ± 12.13%; MPD: -21.50 ± 12.20%) (p < 0.05). For RPE-Set, the scores were smaller for CS2 (RPE8: 3.23 ± 0.61; RPE16: 4.32 ± 1.42; RPE24: 4.46 ± 1.51) compared to TRD (RPE8: 4.73 ± 1.33; RPE16: 5.46 ± 1.62; RPE24: 6.23 ± 1.97) (p = 0.008), as well as for Session RPE (CS2: 4.32 ± 1.59; TRD: 5.68 ± 1.75) (p = 0.015). There were no changes for jump height (CMJ: p = 0.985), and the difference between time points in CMJ (ΔCMJ: p = 0.213) and muscle soreness (DOMS: p = 0.437) were identified. Our findings suggest that using CS with a greater number of intra-set rests is more efficient even with the total rest interval equalized, presenting lower decreases in mechanical performance and lower perceptual effort responses.