Recent research in rodents and humans revealed that Whole-Body Vibration (WBV) is beneficial for cognitive functions. However, the optimal WBV conditions are not established: contrary to vertical WBV, side-alternating WBV was not investigated before. The present study investigated the short-term effects of side-alternating WBV in standing and sitting posture on specific cognitive function of young adults. We used a balanced cross-over design. Sixty healthy young adults (mean age 21.7 ± 2.0 years, 72% female) participated. They were exposed to three bouts of two-minute side-alternating WBV (frequency 27 Hz) and three control conditions in two different sessions. In one session a sitting posture was used and in the other session a standing (semi-squat) posture. After each condition selective attention and inhibition was measured with the incongruent condition of the Stroop Color-Word Interference Test. WBV significantly (p = 0.026) improved selective attention and inhibition in the sitting posture, but not in the standing posture. The sitting posture was perceived as more comfortable, joyous and less exhaustive as compared to the standing posture. This study demonstrated that side-alternating WBV in sitting posture improves selective attention and inhibition in healthy young adults. This indicates that posture moderates the cognitive effect of WBV, although the effects are still small. Future studies should focus on the working mechanisms and further optimization of settings, especially in individuals who are unable to perform active exercise.