This study aimed to evaluate and compare the effects of inertial flywheel training and accentuated eccentric loading training on the neuromuscular performance of well-trained male college sprinters. Fourteen sprinters were recruited and randomly assigned to either the flywheel training (FWT, n = 7) group or the accentuated eccentric loading training (AELT, n = 7) group. The FWT group completed four sets of 2 + 7 repetitions of flywheel squats, whereas the AELT group performed four sets of seven repetitions of barbell squats (concentric/eccentric: 80%/120% 1RM). Both groups underwent an eight-week squat training program, with two sessions per week. A two-way repeated ANOVA analysis was used to find differences between the two groups and between the two testing times (pre-test vs. post-test). The results indicated significant improvements in all measured variables for the FWT group: 1RM (5.0%, ES = 1.28), CMJ (13.3%, ES = 5.42), SJ (6.0%, ES = 2.94), EUR (6.5%, ES = 4.42), SLJ (2.9%, ES = 1.77), and 30 m sprint (−3.4%, ES = −2.80); and for the AELT group: 1RM (6.3%, ES = 2.53), CMJ (7.4%, ES = 3.44), SJ (6.4%, ES = 2.21), SLJ (2.2%, ES = 1.20), and 30 m sprint (−3.0%, ES = −1.84), with the exception of EUR (0.9%, ES = 0.63, p = 0.134), showing no significant difference. In addition, no significant interaction effects between group and time were observed for 1RM back squat, SJ, SLJ, and 30 m sprint (p > 0.05). Conversely, a significant interaction effect between group and time was observed for both CMJ and EUR (p < 0.001); post hoc analysis revealed that the improvements in CMJ and EUR were significantly greater in the FWT group compared to the AELT group (p < 0.001). These findings indicate that both FWT and AELT are effective at enhancing lower-body strength, power, and speed in well-trained male college sprinters, with FWT being particularly more effective in promoting elastic energy storage and the full utilization of the stretch–shortening cycle.