The purpose of this study was to examine the effects of a 6-week combined power-based resistance training (RT) and short sprint interval training (SSIT), performed in different sequences (SSIT+RT or RT+SSIT), on the lower-body physical fitness of male Judo athletes. Twenty-four young male athletes volunteered for this study and were randomly assigned to one of three groups: SSIT+RT, RT+SSIT, or an active control (CON) group, with eight athletes in each group. The training groups participated in a 6-week intervention, training three times per week during the preparatory phase of annual training cycle. Following the intervention, both the SSIT+RT and RT+SSIT groups showed significant improvements (p = 0.001) in several performance measures including vertical jump (effect size [ES] = 1.58 and 0.85), 20-m linear sprint (ES = -1.22 and -0.53), Agility T-test (ES = -1.12 and -0.46), maximal strength (ES = 0.15 and 0.21), Specific Judo Fitness Test (SJFT; ES = -0.91 and -0.90), peak power (ES = 1.74 and 1.18), mean power (ES = 0.98 and 1.11), and cardiorespiratory fitness (ES = 1.17 and 1.03). In contrast, the CON group did not exhibit any significant changes post-training. Moreover, the SSIT+RT group demonstrated significantly greater improvements compared to the RT+SSIT group in vertical jump (ES = 0.62, p = 0.024), 20-m linear sprint (ES = -0.46, p = 0.031), Agility T-test (ES = -0.34, p = 0.016), and peak power output (ES = 0.79, p = 0.009). Conversely, the RT+SSIT group showed more pronounced strength gains than the SSIT+RT group (ES = 0.14, p = 0.007). In conclusion, it is recommended that incorporating SSIT at the beginning of a training session is more effective for improving jumping ability, sprinting speed, change of direction, and peak power output. Conversely, if the primary goal is to enhance muscular strength, it is advisable to prioritize RT at the start of the session.