Background Traditional vertical and side-alternating whole body vibrations (WBV) can effectively improve muscle power performance but have a limited efficacy for enhancing change-of-direction (COD) ability. Novel dual-plate WBV uniquely providing various directions of movements with higher and distinctive frequencies for each leg may cause better acute effect on muscle power and stretch-shortening cycle efficacy contributing to COD ability. Therefore, the purpose of this study was to investigate the acute effect of dual- or single-frequency WBV on squat jumps (SJs), countermovement jumps (CMJs), eccentric utilization ratios (EURs), and COD ability in rugby players. Methods Fourteen male rugby players were recruited and performed a 4 min partial squat with 3 types of WBV protocols on a dual-plate WBV machine, including 1 dual-frequency WBV protocol (DFW) with the dominant leg receiving 35 Hz and the non-dominant leg receiving 45 Hz, and 2 single-frequency WBV protocols (SFWs) with 35 Hz or 45 Hz provided to both legs (SFW35Hz and SFW45Hz) on 3 different days. Results The results showed that all the vibration protocols significantly improved SJ and CMJ performances (SJ: p = 0.008; CMJ: p < 0.001), but did not significantly change EURs (p > 0.05). In addition, only the DFW significantly improved COD ability (p = 0.001 for the pre–post comparison). Conclusion A 4 min dual-frequency WBV session improved both vertical jumping and COD ability in rugby players, suggesting that this could be a potential warm-up protocol for athletes.