Horizontal-speed-deceleration-training (HSDT) has recently emerged as a promising method that specifically targets the eccentric actions of the knee-extensors. This study aimed to compare the effects of replacing a portion of traditional in-season tennis training with HSDT compared to standard training alone on the physical fitness of youth tennis players. Tennis players (n = 23) from two regional tennis teams were assigned to the HSDT-group (n = 14 [8 males, 6 females]; age = 13.24 ± 0.60 years) or to the control-group (n = 9 [6 males, 3 females]; age = 13.08 ± 0.56 years). Before-and- after six weeks of training, participants were assessed for linear 20-m sprint-speed, change-of-direction (COD) speed (505 test), agility (Y-shaped-agility test), jump height/distance (countermovement-jump [CMJ] height; 20-cm drop-jump height; standing-longjump [SLJ] distance), reactive-strength-index (RSI), and repeated-sprint-ability (RSA). ANOVA revealed significant Group-by-Time interactions, indicating greater improvements in the HSDT-group compared to the control-group in 20 m sprint-speed, COD-speed, agility, CMJ-height, SLJ-distance, 20 cm drop-jump height, and RSI (ES = 0.87–2.14; p < 0.05), whereas no significant interaction was observed for RSA outcomes. The HSDT group improved 20-m linear sprint-time (ES = 1.19 [moderate], p < 0.001), COD-speed (ES = 1.19 [moderate], p < 0.001), agility (ES = 2.14 [large], p < 0.01), CMJ-height (ES = 1.42 [large], p < 0.01), SLJ-distance (ES = 1.05 [moderate], p < 0.05), 20-cm drop-jump height (ES = 0.87 [moderate]; p < 0.05), and RSI (ES = 1.71 [large], p < 0.01). However, no significant pre-to-post changes were observed in the group (ES = 0.09 to 0.13; p > 0.05). Replacing part of regular in-season tennis training with HSDT appears to be highly effective in improving multiple physical fitness aspects in youth tennis players. Regular tennis training alone seems insufficient to elicit meaningful gains in these key physical qualities.