Functional training has become a popular training method in different sports, yet limited studies have focused on paddle sports. The purpose of this study was to evaluate the effects of functional training on functional movement and athletic performance in college dragon boat athletes. A total of 42 male athletes were divided into 2 groups: a functional training (FT) group (n = 21, 21 ± 1.47 years) and a regular training (RT) group (n = 21, 22 ± 1.50 years). The FT group participated in an 8-week (16-session) functional-training program, while the RT group trained with strength-training sessions. Functional movement screen (FMS), Y-balance test (YBT) and athletic performance evaluations were conducted before and after the intervention. Repeated measure ANOVA and t-test evaluations were employed to examine differences for both groups. The FT group was significantly improved in FMS scores (F = 0.191, p < 0.001) and YBT scores (F = 2.59, p = 0.027), and it also showed significantly improved muscular fitness (pull-ups: F = 0.127, p < 0.001; push-ups: F = 1.43, p < 0.001) and rowing speed (F = 4.37, p = 0.004). It is recommended to include functional training as a part of training and routine exercise, as it appears to be an effective way of improving FMS and athletic performance in paddle sports.