Background Although progressive core stabilization training (PCST) improves sport-specific abilities, the effects of PCST on anaerobic performance and fatigue are still unclear today. Therefore, this prospective, single-blind (blinded: athletes, using placebo intervention), randomized (using random selection method) controlled study aimed to investigate the presence of these effects in elite athletes. Methods Athletes were randomly assigned to intervention (n = 30, 21.70 ± 2.71 years) and control (n = 28, 21.71 ± 2.49 years) groups in this study. While standard core strengthening exercises (SCSE) (3 days/week for a total of 9 weeks) were given to the control group, PCST (3 days/week for a total of 9 weeks) was applied to the intervention group. Anaerobic capacity, anaerobic power, and fatigue index were evaluated using 30-second (s) Wingate Anaerobic Power test and vertical jump tests. The intra-group and inter-group changes in anaerobic power, anaerobic capacity, fatigue index, and jump variables were shown using Paired Sample T Test and Independent-Samples T Test, respectively. Results After a 9-week training, while intra-group difference (delta) values before and after interventions for maximum anaerobic power, maximum anaerobic capacity, anaerobic power between 0 and 5 s, anaerobic capacity between 0 and 30 s, anaerobic power values at the 5th (effect size d: 0.67), 10th and 15th sec, and vertical countermovement jump (effect size d: 0.54) increased significantly more in the intervention group compared to control group, delta values for anaerobic power at the 20th and 25th sec increased significantly in control group compared to intervention group (p < 0.05). No significant differences were found in delta values for minimum anaerobic power, 30th sec anaerobic power, fatigue index and vertical squat jump between groups (p > 0.05). Conclusions PCST appears to be more effective than SCSE in enhancing anaerobic capacity and early-phase anaerobic power in elite athletes. While SCSE contributes to improvements in anaerobic power during the later stages of the Wingate test, PCST provides broader and more functionally relevant gains across key performance metrics. Therefore, PCST should be prioritized and integrated into athletic training programs aimed at improving overall anaerobic performance and optimizing athletic potential in elite athletes in taekwondo, weightlifting, volleyball, and badminton. Clinical trail trial registration This study was retrospectively registered as a clinical trial with registration number NCT06042374 on 30/08/2023.
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