The purpose of this study was to explore the immediate effects of different frequencies of whole-body vibration (WBV) on the performance of trunk muscles of healthy young adults. A group of 30 healthy subjects (15 men; 15 women; age, 26.8 ± 3.74 years; body mass index, 21.9 ± 1.802) participated in the study. Each subject received 3 sessions of vibration exercise with different exercise parameters with frequencies of 25 Hz and 40 Hz and sham stimulation in a random order on different days. Before and after each WBV exercise session, subjects were assessed for trunk muscle strength/endurance tests and trunk proprioception tests. There was a significant increase in trunk extensor strength (p ≤ 0.05) after low-frequency (25 Hz) WBV exercise, but high-frequency (40 Hz) vibration exercise had resulted in a significant decrease in trunk extensor endurance (p ≤ 0.05). Statistical gender difference (p = 0.04) was found for trunk extensor endurance with lower WBV training. No change was noted in the trunk proprioception with different frequencies of WBV. In conclusions, the immediate response of the body to WBV was different for low and high frequencies. Low-frequency vibration enhanced trunk extensor strength, but high-frequency vibration would decrease endurance of the trunk extensor muscles. Males are more sensitive than females in trunk extensor endurance for lower frequency WBV exposure. These results indicated that short-term WBV with low frequency was effective to improve trunk extensor strength in healthy adults, and that could be helpful for relevant activities of trunk extensor performing and preventing sport injury.