Background: Brazilian Jiu-Jitsu (BJJ) athletes often engage in high-intensity, intermittent bouts requiring rapid neuromuscular responses. Inter-set cooling strategies, such as foot cooling (FC), have been proposed to enhance recovery and performance in various sports. However, the efficacy of FC in BJJ-specific anaerobic performance remains unclear. Methods: Thirteen male BJJ athletes participated in a randomized crossover study, performing the Jiu-Jitsu Anaerobic Performance Test (JJAPT) under two conditions: with FC and without (CON). Each session comprised three sets of maximal effort, with heart rate (HR) and rating of perceived exertion (RPE) recorded post-set. FC involved immersing the feet in cold water (10 ◦C) for 2 minutes between sets. Results: Total repetitions were significantly lower in FC condition compared to control condition (FC: 268.1 ± 32.8; CON: 277.3 ± 27.7; p = 0.024, effect size (ES) = 0.15). Both conditions exhibited a significant decline in repetitions across sets (p < 0.001), indicating fatigue. HR increased significantly from Set 1 to Sets 2 and 3 in both conditions (p < 0.05), with no significant differences between conditions. Similarly, RPE scores rose across sets (p < 0.001), with no significant differences between FC and control. Conclusions: Inter-set foot cooling decreased the anaerobic performance without change HR, or RPE in BJJ athletes during the JJAPT. These findings suggest that FC may not be an effective recovery strategy in BJJ contexts, potentially due to the sport’s reliance on rapid neuromuscular function, which could be impaired by peripheral cooling. Further research should explore alternative cooling methods that align with the specific demands of BJJ.